CRAN Package Check Results for Package SafeQuant

Last updated on 2020-04-09 09:48:26 CEST.

Check Details

Version: 2.3.1
Check: tests
Result: ERROR
     Running 'initTestSession.R' [16s/18s]
     Running 'runAllTest.R' [0s/0s]
     Running 'testExpressionAnalysis.R' [16s/18s]
     Running 'testGraphics.R' [24s/27s]
     Running 'testIdentificationAnalysis.R' [17s/20s]
     Running 'testParser.R' [19s/21s]
     Running 'testSafeQuantAnalysis.R' [24s/27s]
     Running 'testTMT.R' [16s/19s]
     Running 'testUserOptions.R' [16s/18s]
    Running the tests in 'tests/testExpressionAnalysis.R' failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testCreateExpressionDataset <- function(){
     +
     + cat("--- testCreateExpressionDataset: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     + cat("--- testCreateExpressionDataset: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > testGetAllEBayes <- function(){
     +
     +
     + cat("--- testGetAllEBayes: --- \n")
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + pAdj <- getAllEBayes(eset, adjust=T)
     +
     + stopifnot( mean(pAdj[,"A"]) > mean(p[,"A"]) )
     +
     + ### paired desgn
     + esetNonPaired <- esetPaired
     + pData(esetNonPaired) <- pData(esetPaired)[,1:2]
     +
     + pValPaired <- getAllEBayes(esetPaired,adjust=F,method=c("all"))
     + pValPairedPairwise <- getAllEBayes(esetPaired,adjust=F,method=c("pairwise"))
     +
     + pValNonPaired <- getAllEBayes(esetNonPaired,adjust=F,method=c("all"))
     + pValNonPairedPairwise <- getAllEBayes(esetNonPaired,adjust=F,method=c("pairwise"))
     + stopifnot(all(apply(pValPaired,2,sum) < apply(pValNonPaired,2,sum)))
     + stopifnot(all(apply(pValPairedPairwise,2,sum) < apply(pValNonPairedPairwise,2,sum)))
     +
     + # adjustment filter
     +
     + adjustfilter <- data.frame(rep(T,nrow(eset)),rep(T,nrow(eset)) )
     + adjustfilter[1,1] <- F
     + adjustfilter[2,2] <- F
     +
     + pTmp <- getAllEBayes(eset,adjust=T, adjustFilter=adjustfilter)
     + stopifnot(p[1,1] == pTmp[1,1])
     + stopifnot(p[2,2] == pTmp[2,2])
     + stopifnot(is.na(pTmp[3,2]))
     + cat("--- testGetAllEBayes: PASS ALL TEST --- \n")
     +
     + # Question: limma multiple groups comparison produces different pvalue comparing with two group comparsion
     + # https://support.bioconductor.org/p/44216/
     + # https://support.bioconductor.org/p/60556/
     + }
     >
     > testGetRatios <- function(){
     +
     + cat("--- testGetRatios: --- \n")
     +
     + r <- getRatios(eset)
     +
     + exprs(eset)[1,c(5:6,1:2)]
     + # C_rep_1 C_rep_2 A_rep_1 A_rep_2
     + # 9.963852 9.966003 9.965568 9.967214
     +
     + ## NOTE: C is control
     + stopifnot(all.equal(r[1,1],median(log2(exprs(eset))[1,1:2]) - median(log2(exprs(eset))[1,5:6]) ) )
     +
     + stopifnot(mean(r[,"A"]) < mean(r[,"B"]))
     + stopifnot(all.equal(r,getRatios(eset,method="mean")))
     + r <- getRatios(eset)
     + stopifnot(all.equal(mean(r[,"B"]),mean(r[,"B"])))
     +
     + stopifnot(all(round(apply(getRatios(esetPaired, log2=F),2,mean),1) == c(1.5,1.2)))
     + stopifnot(ncol(r) == 2)
     +
     + rPaired <- getRatios(esetPaired, method="paired")
     + stopifnot(ncol(rPaired) == 4)
     + stopifnot(all( log2(exprs(esetPaired)[,1]) - log2(exprs(esetPaired)[,5]) == rPaired[,1] ))
     + stopifnot(all( log2(exprs(esetPaired)[,4]) - log2(exprs(esetPaired)[,6]) == rPaired[,4] ))
     + stopifnot(all( exprs(esetPaired)[,4] / exprs(esetPaired)[,6] == getRatios(esetPaired, method="paired", log2=F)[,4] ))
     + # should fail
     + stopifnot((inherits(try( getRatios(eset, method="paired"), silent = TRUE), "try-error")))
     +
     +
     + stopifnot(all(round(getRatios(esetPaired)[,1],2) == round(apply(rPaired[,1:2],1,median),2)))
     +
     +
     + cat("--- testGetRatios: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetAllCV <- function(){
     +
     + cat("--- testGetAllCV: --- \n")
     +
     + cv <- getAllCV(eset)
     +
     + stopifnot(all.equal(cv[1,"A"] , (sd(exprs(eset)[1,unlist(pData(eset)$condition == "A")]) / mean(exprs(eset)[1,unlist(pData(eset)$condition == "A")]))))
     + stopifnot(all.equal(cv[200,"C"] , sd(exprs(eset)[200,unlist(pData(eset)$condition == "C")]) / mean(exprs(eset)[200,unlist(pData(eset)$condition == "C")])))
     +
     + cvPaired <- getAllCV(esetPaired)
     + stopifnot(all(is.na(cvPaired[,1])))
     + stopifnot(all(!is.na(cvPaired[,2])))
     + stopifnot(cvPaired[3,"A"] == (sd(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6]) / mean(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6])))
     +
     + cat("--- testGetAllCV: PASS ALL TEST --- \n")
     + }
     >
     > testGlobalNormalize <- function(){
     +
     + cat("--- testGlobalNormalize: --- \n")
     +
     + globalNormFactors <- getGlobalNormFactors(eset,method="sum")
     + ### add normalization factors to ExpressionSet
     + pData(eset) <- cbind(pData(eset),globalNormFactors)
     + esetNorm <- globalNormalize(eset,globalNormFactors)
     +
     + stopifnot(all.equal(as.vector(unlist(apply(exprs(esetNorm),2,sum))),as.vector(rev(unlist(apply(exprs(esetNorm),2,sum))))))
     +
     + stopifnot(pData(esetNorm)$normFactor[1] == 1)
     + stopifnot(pData(esetNorm)$normFactor[2] != 1)
     +
     + cat("--- testGlobalNormalize: PASS ALL TEST --- \n")
     +
     + # Should generate error and stop
     + # fData(eset)$isNormAnchor <- rep(F,nrow(eset))
     + # esetNorm <- normalizeIntensities(eset)
     +
     + }
     >
     > testGetSignalPerCondition <- function(){
     +
     + cat("--- testGetSignalPerCondition: --- \n")
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"A"] <= getSignalPerCondition(eset,method="max")[,"A"]) == nrow(eset))
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"C"] <= getSignalPerCondition(eset,method="median")[,"C"]) == nrow(eset))
     + stopifnot(getSignalPerCondition(eset,method="sd")[1,2] == sd(exprs(eset)[1,3:4]))
     + cat("--- testGetSignalPerCondition: PASS ALL TEST --- \n")
     + }
     >
     > testBaselineIntensity <- function(){
     +
     + cat("--- testBaselineIntensity: --- \n")
     +
     + allInt <- as.vector(unlist(exprs(eset)))
     + bl <- round(getBaselineIntensity(allInt,promille=5),2)
     + #hist(allInt)
     + #abline(v=bl,lwd=2)
     + stopifnot(all.equal(bl[[1]] , 997.82) )
     +
     +
     + set.seed(1234)
     + suppressWarnings(allInt2 <- log10(rnorm(1000,1,1)))
     + bl2 <- round(getBaselineIntensity(allInt2,promille=5),2)
     + stopifnot(all.equal(-1.95,bl2[[1]]))
     + #hist(allInt2)
     + #abline(v=bl2,lwd=2)
     +
     + cat("--- testBaselineIntensity: PASS ALL TEST --- \n")
     +
     + }
     >
     > testRollUp <- function(){
     +
     + cat(" --- testRollUp --- \n")
     +
     + rollUpEset1 <- rollUp(eset,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$proteinName ) ) == nrow(rollUpEset1))
     +
     + rollUpEset2 <- rollUp(eset ,featureDataColumnName= c("ptm"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset2))
     +
     + rollUpEset3 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("ptm"), method=c("mean"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset3))
     +
     + #print(exprs(rollUpEset2))
     +
     + stopifnot(all.equal(sum(exprs(rollUpEset2)),sum(exprs(rollUpEset1)))) ### test sum
     + stopifnot(sum(exprs(rollUpEset1)) != sum(exprs(rollUpEset3))) ### test mean
     +
     + rollUpEset4 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))
     + stopifnot(sum(exprs(rollUpEset3)) != sum(exprs(rollUpEset4)) ) ### test top 3
     +
     + cat(" --- testRollUp: PASS ALL TEST --- \n")
     +
     + # progenesisFeatureCsvFile3 <- "/Users/ahrnee-adm/dev/R/workspace/SafeQuant/inst/testData/2014/peptides2.csv"
     + # d <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile3,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile3))
     + # system.time(e <- rollUp(d, method="sum", isProgressBar=T, featureDataColumnName= c("peptide")))
     + # system.time(e <- rollUpDT(d, method="sum", featureDataColumnName= c("peptide")))
     + #
     + esetTmp <- parseProgenesisPeptideMeasurementCsv(progenesisPeptideMeasurementCsvFile1,expDesign= getExpDesignProgenesisCsv(progenesisPeptideMeasurementCsvFile1))
     +
     + fData(esetTmp)
     +
     + rollUpEsetProteinAllAccessions <- rollUp(esetTmp,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot(fData(rollUpEsetProteinAllAccessions)$allAccessionsTMP[68] == "sp|E9PAV3|NACAM_HUMAN;sp|Q9BZK3|NACP1_HUMAN")
     +
     + }
     >
     > testTopX <- function(){
     +
     + cat(" --- testTopX --- \n")
     +
     + entryData1 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,5),ncol=4)))
     + rownames(entryData1) <- paste("peptide",1:nrow(entryData1),sep="_")
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 5
     + stopifnot(all.equal(rep(10/3,3) , as.vector(unlist(getTopX(entryData1))) ))
     +
     + entryData2 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,NA),ncol=4)))
     + rownames(entryData2) <- paste("peptide",1:nrow(entryData2),sep="_")
     +
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 NA
     + stopifnot(all.equal(c(4,4,3) , as.vector(unlist(getTopX(entryData2,topX=2)))))
     +
     + # 1 row
     + stopifnot(all.equal(rep(1,3),as.vector(unlist(getTopX(entryData1[1,])))))
     +
     + # 1 col
     + stopifnot(all.equal(getTopX(entryData1)[[1]],getTopX(entryData1[,1])))
     +
     + top1 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top1"))),1,sum)
     + top3 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))),1,sum)
     + meanInt <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("mean"))),1,sum)
     +
     + stopifnot(sum(top1 >= top3 ) == length(top3))
     + stopifnot(sum(top1) > sum(top3))
     + stopifnot(sum(top1) > sum(meanInt))
     + stopifnot(all.equal(sum(top3),sum(meanInt)))
     +
     + cat(" --- testTopX: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetIBAQEset <- function(){
     +
     + cat(" --- testGetIBAQEset --- \n")
     +
     + # read protein fasta
     + proteinDB <- read.fasta(fastaFile,seqtype = "AA",as.string = TRUE, set.attributes = FALSE)
     +
     + iBaqEset <- getIBAQEset(eset,proteinDB=proteinDB)
     + stopifnot(round(exprs(iBaqEset))[1,1] == 125)
     + stopifnot(round(exprs(iBaqEset))[2,2] == 38)
     +
     + cat(" --- testGetIBAQEset: PASS ALL TEST --- \n")
     + }
     >
     >
     > testGetLoocvFoldError <- function(){
     +
     + cat(" --- testGetLoocvFoldError --- \n")
     + #plotCalibrationCurve(fit)
     + stopifnot( round(sum(getLoocvFoldError(absEstSimData))) == -8)
     + cat(" --- testGetLoocvFoldError: PASS ALL TEST --- \n")
     + }
     >
     > testSqNormalize <- function(){
     +
     + cat(" --- testSqNormalize --- \n")
     +
     + stopifnot(nrow(sqNormalize(eset, method = "global")) == 900)
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + stopifnot(nrow(sqNormalize(esetTmp, method = "rt")) == 496)
     +
     + cat(" --- testSqNormalize: PASS ALL TEST --- \n")
     + }
     >
     >
     > testRtNormalize <- function(){
     +
     +
     + cat(" --- testRTNormalize --- \n")
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + rtNormFactors <- getRTNormFactors(esetTmp, minFeaturesPerBin=100)
     + stopifnot(nrow(rtNormalize(esetTmp,rtNormFactors)) == 97)
     +
     + # Stop if rtNormFactors doesn't cover all retention times.
     + #rtNormalize(esetTmp,rtNormFactors[1:2,])
     +
     + cat(" --- testRTNormalize: PASS ALL TEST --- \n")
     + }
     >
     > testRemoveOutliers <- function(){
     +
     + cat(" --- testRemoveOutliers --- \n")
     + set.seed(1234)
     + stopifnot(sum(is.na(removeOutliers(c(-10, rnorm(100), 10)))) == 2)
     + cat(" --- testRemoveOutliers: PASS ALL TEST --- \n")
     + }
     >
     > testPerFeatureNormalization <- function(){
     +
     + cat(" --- testPerFeatureNormalization: --- \n")
     +
     + normFactors <- exprs(eset)[1:10,1:3]
     + colnames(normFactors) <- c("A","B","C")
     + rownames(normFactors) <- fData(eset)[1:10,]$proteinName
     + normFactors[is.finite(normFactors)] <- 1
     + eNorm <- perFeatureNormalization(eset,normFactors)
     +
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,2] , (exprs(eset)[1,2]-1)))
     + stopifnot(all.equal(exprs(eNorm)[13,2] , (exprs(eset)[13,2])))
     +
     + normFactors[,2] <- 200
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,3] , (exprs(eset)[1,3]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,4] , (exprs(eset)[1,4]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,5] , (exprs(eset)[1,5]-1)))
     +
     + normFactors[,3] <- 0
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,5] , exprs(eset)[1,5]))
     + stopifnot(all.equal(exprs(eNorm)[2,6] , exprs(eset)[2,6]))
     +
     + normFactors[3,] <- 1000
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + # re-order normFactors columns
     + eNorm <- perFeatureNormalization(eset,normFactors[,rev(colnames(normFactors))])
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + cat(" --- testPerFeatureNormalization: PASS ALL TEST --- \n")
     +
     + #coveredPeptideSel <- fData(eset)$proteinName %in% rownames(normFactors)
     + #exprs(eset)[coveredPeptideSel,] <- exprs(eset)[coveredPeptideSel, ] - normFactors[as.character(fData(eset)[coveredPeptideSel,]$proteinName),pData(eset)$condition]
     +
     + }
     >
     >
     > testStandardise <- function(){
     +
     + cat(" --- testStandardise: --- \n")
     +
     + d <- data.frame(rnorm(10000,5,20), rnorm(10000,10,10))
     + dStd <- standardise(d[,1])
     +
     + stopifnot(round(mean(dStd)) == 0 )
     + stopifnot(round(sd(dStd)) == 1 )
     +
     + dStd <- standardise(d)
     + stopifnot(round(apply(dStd,2,mean)[1]) == 0)
     + stopifnot(round(apply(dStd,2,sd)[1]) == 1)
     +
     + cat(" --- testStandardise: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetMaxIndex <-function(){
     +
     + cat(" --- testGetMaxIndex: --- \n")
     + d <- data.frame(s=c(NA,NA,NA,NA,1,1:4),lab=sort(rep(c("A","B","C"),3)))
     + DT <- data.table(d)
     + setkey(DT,lab)
     +
     +
     + stopifnot(all.equal(c(1,5,9) , DT[, .I[getMaxIndex(s)], by=lab ]$V1 ))
     + cat(" --- testGetMaxIndex: PASS ALL TEST --- \n")
     +
     + }
     >
     > testCreatePairedExpDesign <- function(){
     +
     + cat(" --- testCreatePairedExpDesign: --- \n")
     + stopifnot(all( pData(createPairedExpDesign(eset))$subject == as.factor(rep(1:2,3))))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:3]), silent = TRUE), "try-error")))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:4]), silent = TRUE), "ExpressionSet")))
     + cat(" --- testCreatePairedExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     > ### TEST FUNCTIONS END
     >
     > #### TESTS
     > #testGetRatios()
     > #testGetAllEBayes()
     > #testGetSignalPerCondition()
     > #testGetRatios()
     >
     > if(T){
     + testCreateExpressionDataset()
     + testGetAllEBayes()
     + testGetRatios()
     + testGetAllCV()
     + testGlobalNormalize()
     + #testNormalise()
     + testRtNormalize()
     +
     + testBaselineIntensity()
     + testRollUp()
     + testTopX()
     +
     + testGetLoocvFoldError()
     +
     + testRemoveOutliers()
     + testPerFeatureNormalization()
     + testStandardise()
     + testGetMaxIndex()
     +
     + testGetIBAQEset()
     +
     + testCreatePairedExpDesign()
     +
     + }
     --- testCreateExpressionDataset: ---
     Error in testCreateExpressionDataset() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testCreateExpressionDataset -> stopifnot
     Execution halted
    Running the tests in 'tests/testUserOptions.R' failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     >
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testExpDesignTagToExpDesign <- function(){
     +
     + cat("--- testExpDesignTagToExpDesign: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     +
     + expDesignString1 <- "1,2,3:4,5,6"
     +
     + # 6-plex default: 1,2,3:4,5,6
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 1 TRUE
     + #3 Condition 1 TRUE
     + #4 Condition 2 FALSE
     + #5 Condition 2 FALSE
     + #6 Condition 2 FALSE
     +
     +
     + expDesign <- data.frame(condition=paste("Condition",sort(rep(c(1,2),3))),isControl=sort(rep(c(T,F),3),decreasing=T) )
     +
     + expDesign1 <- expDesignTagToExpDesign(expDesignString1, expDesign)
     +
     + stopifnot(nrow(expDesign1) == 6 )
     + stopifnot(length(unique(expDesign1$condition)) == 2 )
     + stopifnot(sum(expDesign1$isControl) == 3 )
     +
     + expDesignString2 <- "1,4,7,10:2,5,8:3,6,9"
     +
     + # 10-plex default is "1,4,7,10:2,5,8:3,6,9"
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 2 FALSE
     + #3 Condition 3 FALSE
     + #4 Condition 1 TRUE
     + #5 Condition 2 FALSE
     + #6 Condition 3 FALSE
     + #7 Condition 1 TRUE
     + #8 Condition 2 FALSE
     + #9 Condition 3 FALSE
     + #10 Condition 1 TRUE
     +
     + expDesign <- data.frame(condition=paste("Condition",c(1,2,3,1,2,3,1,2,3,1)),isControl=c(T,F,F,T,F,F,T,F,F,T) )
     + expDesign2 <- expDesignTagToExpDesign(expDesignString2, expDesign)
     + stopifnot(nrow(expDesign2) == 10 )
     + stopifnot(length(unique(expDesign2$condition)) == 3 )
     + stopifnot(sum(expDesign2$isControl) == 4 )
     +
     + ### condition name assignment when mixing runs from different conditions
     + expDesign <- data.frame(condition=paste("foo",c(1,1,1,2,2,3,3)),isControl=c(F,F,F,T,T,F,F) )
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5:6",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1:4,6:5",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1,2,4",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("2",expDesign)$condition)))
     + stopifnot( length(unique(expDesignTagToExpDesign("1:2:3:4:5:6",expDesign)$condition)) == 6)
     +
     + cat("--- testExpDesignTagToExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > ### TEST FUNCTIONS END
     >
     > ### TESTS
     > testExpDesignTagToExpDesign()
     --- testExpDesignTagToExpDesign: ---
     Error in testExpDesignTagToExpDesign() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testExpDesignTagToExpDesign -> stopifnot
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.3.1
Check: tests
Result: ERROR
     Running ‘initTestSession.R’ [10s/14s]
     Running ‘runAllTest.R’ [0s/1s]
     Running ‘testExpressionAnalysis.R’ [10s/15s]
     Running ‘testGraphics.R’ [16s/26s]
     Running ‘testIdentificationAnalysis.R’ [11s/17s]
     Running ‘testParser.R’ [12s/18s]
     Running ‘testSafeQuantAnalysis.R’ [15s/24s]
     Running ‘testTMT.R’ [10s/16s]
     Running ‘testUserOptions.R’ [10s/15s]
    Running the tests in ‘tests/testExpressionAnalysis.R’ failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testCreateExpressionDataset <- function(){
     +
     + cat("--- testCreateExpressionDataset: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     + cat("--- testCreateExpressionDataset: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > testGetAllEBayes <- function(){
     +
     +
     + cat("--- testGetAllEBayes: --- \n")
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + pAdj <- getAllEBayes(eset, adjust=T)
     +
     + stopifnot( mean(pAdj[,"A"]) > mean(p[,"A"]) )
     +
     + ### paired desgn
     + esetNonPaired <- esetPaired
     + pData(esetNonPaired) <- pData(esetPaired)[,1:2]
     +
     + pValPaired <- getAllEBayes(esetPaired,adjust=F,method=c("all"))
     + pValPairedPairwise <- getAllEBayes(esetPaired,adjust=F,method=c("pairwise"))
     +
     + pValNonPaired <- getAllEBayes(esetNonPaired,adjust=F,method=c("all"))
     + pValNonPairedPairwise <- getAllEBayes(esetNonPaired,adjust=F,method=c("pairwise"))
     + stopifnot(all(apply(pValPaired,2,sum) < apply(pValNonPaired,2,sum)))
     + stopifnot(all(apply(pValPairedPairwise,2,sum) < apply(pValNonPairedPairwise,2,sum)))
     +
     + # adjustment filter
     +
     + adjustfilter <- data.frame(rep(T,nrow(eset)),rep(T,nrow(eset)) )
     + adjustfilter[1,1] <- F
     + adjustfilter[2,2] <- F
     +
     + pTmp <- getAllEBayes(eset,adjust=T, adjustFilter=adjustfilter)
     + stopifnot(p[1,1] == pTmp[1,1])
     + stopifnot(p[2,2] == pTmp[2,2])
     + stopifnot(is.na(pTmp[3,2]))
     + cat("--- testGetAllEBayes: PASS ALL TEST --- \n")
     +
     + # Question: limma multiple groups comparison produces different pvalue comparing with two group comparsion
     + # https://support.bioconductor.org/p/44216/
     + # https://support.bioconductor.org/p/60556/
     + }
     >
     > testGetRatios <- function(){
     +
     + cat("--- testGetRatios: --- \n")
     +
     + r <- getRatios(eset)
     +
     + exprs(eset)[1,c(5:6,1:2)]
     + # C_rep_1 C_rep_2 A_rep_1 A_rep_2
     + # 9.963852 9.966003 9.965568 9.967214
     +
     + ## NOTE: C is control
     + stopifnot(all.equal(r[1,1],median(log2(exprs(eset))[1,1:2]) - median(log2(exprs(eset))[1,5:6]) ) )
     +
     + stopifnot(mean(r[,"A"]) < mean(r[,"B"]))
     + stopifnot(all.equal(r,getRatios(eset,method="mean")))
     + r <- getRatios(eset)
     + stopifnot(all.equal(mean(r[,"B"]),mean(r[,"B"])))
     +
     + stopifnot(all(round(apply(getRatios(esetPaired, log2=F),2,mean),1) == c(1.5,1.2)))
     + stopifnot(ncol(r) == 2)
     +
     + rPaired <- getRatios(esetPaired, method="paired")
     + stopifnot(ncol(rPaired) == 4)
     + stopifnot(all( log2(exprs(esetPaired)[,1]) - log2(exprs(esetPaired)[,5]) == rPaired[,1] ))
     + stopifnot(all( log2(exprs(esetPaired)[,4]) - log2(exprs(esetPaired)[,6]) == rPaired[,4] ))
     + stopifnot(all( exprs(esetPaired)[,4] / exprs(esetPaired)[,6] == getRatios(esetPaired, method="paired", log2=F)[,4] ))
     + # should fail
     + stopifnot((inherits(try( getRatios(eset, method="paired"), silent = TRUE), "try-error")))
     +
     +
     + stopifnot(all(round(getRatios(esetPaired)[,1],2) == round(apply(rPaired[,1:2],1,median),2)))
     +
     +
     + cat("--- testGetRatios: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetAllCV <- function(){
     +
     + cat("--- testGetAllCV: --- \n")
     +
     + cv <- getAllCV(eset)
     +
     + stopifnot(all.equal(cv[1,"A"] , (sd(exprs(eset)[1,unlist(pData(eset)$condition == "A")]) / mean(exprs(eset)[1,unlist(pData(eset)$condition == "A")]))))
     + stopifnot(all.equal(cv[200,"C"] , sd(exprs(eset)[200,unlist(pData(eset)$condition == "C")]) / mean(exprs(eset)[200,unlist(pData(eset)$condition == "C")])))
     +
     + cvPaired <- getAllCV(esetPaired)
     + stopifnot(all(is.na(cvPaired[,1])))
     + stopifnot(all(!is.na(cvPaired[,2])))
     + stopifnot(cvPaired[3,"A"] == (sd(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6]) / mean(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6])))
     +
     + cat("--- testGetAllCV: PASS ALL TEST --- \n")
     + }
     >
     > testGlobalNormalize <- function(){
     +
     + cat("--- testGlobalNormalize: --- \n")
     +
     + globalNormFactors <- getGlobalNormFactors(eset,method="sum")
     + ### add normalization factors to ExpressionSet
     + pData(eset) <- cbind(pData(eset),globalNormFactors)
     + esetNorm <- globalNormalize(eset,globalNormFactors)
     +
     + stopifnot(all.equal(as.vector(unlist(apply(exprs(esetNorm),2,sum))),as.vector(rev(unlist(apply(exprs(esetNorm),2,sum))))))
     +
     + stopifnot(pData(esetNorm)$normFactor[1] == 1)
     + stopifnot(pData(esetNorm)$normFactor[2] != 1)
     +
     + cat("--- testGlobalNormalize: PASS ALL TEST --- \n")
     +
     + # Should generate error and stop
     + # fData(eset)$isNormAnchor <- rep(F,nrow(eset))
     + # esetNorm <- normalizeIntensities(eset)
     +
     + }
     >
     > testGetSignalPerCondition <- function(){
     +
     + cat("--- testGetSignalPerCondition: --- \n")
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"A"] <= getSignalPerCondition(eset,method="max")[,"A"]) == nrow(eset))
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"C"] <= getSignalPerCondition(eset,method="median")[,"C"]) == nrow(eset))
     + stopifnot(getSignalPerCondition(eset,method="sd")[1,2] == sd(exprs(eset)[1,3:4]))
     + cat("--- testGetSignalPerCondition: PASS ALL TEST --- \n")
     + }
     >
     > testBaselineIntensity <- function(){
     +
     + cat("--- testBaselineIntensity: --- \n")
     +
     + allInt <- as.vector(unlist(exprs(eset)))
     + bl <- round(getBaselineIntensity(allInt,promille=5),2)
     + #hist(allInt)
     + #abline(v=bl,lwd=2)
     + stopifnot(all.equal(bl[[1]] , 997.82) )
     +
     +
     + set.seed(1234)
     + suppressWarnings(allInt2 <- log10(rnorm(1000,1,1)))
     + bl2 <- round(getBaselineIntensity(allInt2,promille=5),2)
     + stopifnot(all.equal(-1.95,bl2[[1]]))
     + #hist(allInt2)
     + #abline(v=bl2,lwd=2)
     +
     + cat("--- testBaselineIntensity: PASS ALL TEST --- \n")
     +
     + }
     >
     > testRollUp <- function(){
     +
     + cat(" --- testRollUp --- \n")
     +
     + rollUpEset1 <- rollUp(eset,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$proteinName ) ) == nrow(rollUpEset1))
     +
     + rollUpEset2 <- rollUp(eset ,featureDataColumnName= c("ptm"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset2))
     +
     + rollUpEset3 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("ptm"), method=c("mean"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset3))
     +
     + #print(exprs(rollUpEset2))
     +
     + stopifnot(all.equal(sum(exprs(rollUpEset2)),sum(exprs(rollUpEset1)))) ### test sum
     + stopifnot(sum(exprs(rollUpEset1)) != sum(exprs(rollUpEset3))) ### test mean
     +
     + rollUpEset4 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))
     + stopifnot(sum(exprs(rollUpEset3)) != sum(exprs(rollUpEset4)) ) ### test top 3
     +
     + cat(" --- testRollUp: PASS ALL TEST --- \n")
     +
     + # progenesisFeatureCsvFile3 <- "/Users/ahrnee-adm/dev/R/workspace/SafeQuant/inst/testData/2014/peptides2.csv"
     + # d <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile3,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile3))
     + # system.time(e <- rollUp(d, method="sum", isProgressBar=T, featureDataColumnName= c("peptide")))
     + # system.time(e <- rollUpDT(d, method="sum", featureDataColumnName= c("peptide")))
     + #
     + esetTmp <- parseProgenesisPeptideMeasurementCsv(progenesisPeptideMeasurementCsvFile1,expDesign= getExpDesignProgenesisCsv(progenesisPeptideMeasurementCsvFile1))
     +
     + fData(esetTmp)
     +
     + rollUpEsetProteinAllAccessions <- rollUp(esetTmp,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot(fData(rollUpEsetProteinAllAccessions)$allAccessionsTMP[68] == "sp|E9PAV3|NACAM_HUMAN;sp|Q9BZK3|NACP1_HUMAN")
     +
     + }
     >
     > testTopX <- function(){
     +
     + cat(" --- testTopX --- \n")
     +
     + entryData1 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,5),ncol=4)))
     + rownames(entryData1) <- paste("peptide",1:nrow(entryData1),sep="_")
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 5
     + stopifnot(all.equal(rep(10/3,3) , as.vector(unlist(getTopX(entryData1))) ))
     +
     + entryData2 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,NA),ncol=4)))
     + rownames(entryData2) <- paste("peptide",1:nrow(entryData2),sep="_")
     +
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 NA
     + stopifnot(all.equal(c(4,4,3) , as.vector(unlist(getTopX(entryData2,topX=2)))))
     +
     + # 1 row
     + stopifnot(all.equal(rep(1,3),as.vector(unlist(getTopX(entryData1[1,])))))
     +
     + # 1 col
     + stopifnot(all.equal(getTopX(entryData1)[[1]],getTopX(entryData1[,1])))
     +
     + top1 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top1"))),1,sum)
     + top3 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))),1,sum)
     + meanInt <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("mean"))),1,sum)
     +
     + stopifnot(sum(top1 >= top3 ) == length(top3))
     + stopifnot(sum(top1) > sum(top3))
     + stopifnot(sum(top1) > sum(meanInt))
     + stopifnot(all.equal(sum(top3),sum(meanInt)))
     +
     + cat(" --- testTopX: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetIBAQEset <- function(){
     +
     + cat(" --- testGetIBAQEset --- \n")
     +
     + # read protein fasta
     + proteinDB <- read.fasta(fastaFile,seqtype = "AA",as.string = TRUE, set.attributes = FALSE)
     +
     + iBaqEset <- getIBAQEset(eset,proteinDB=proteinDB)
     + stopifnot(round(exprs(iBaqEset))[1,1] == 125)
     + stopifnot(round(exprs(iBaqEset))[2,2] == 38)
     +
     + cat(" --- testGetIBAQEset: PASS ALL TEST --- \n")
     + }
     >
     >
     > testGetLoocvFoldError <- function(){
     +
     + cat(" --- testGetLoocvFoldError --- \n")
     + #plotCalibrationCurve(fit)
     + stopifnot( round(sum(getLoocvFoldError(absEstSimData))) == -8)
     + cat(" --- testGetLoocvFoldError: PASS ALL TEST --- \n")
     + }
     >
     > testSqNormalize <- function(){
     +
     + cat(" --- testSqNormalize --- \n")
     +
     + stopifnot(nrow(sqNormalize(eset, method = "global")) == 900)
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + stopifnot(nrow(sqNormalize(esetTmp, method = "rt")) == 496)
     +
     + cat(" --- testSqNormalize: PASS ALL TEST --- \n")
     + }
     >
     >
     > testRtNormalize <- function(){
     +
     +
     + cat(" --- testRTNormalize --- \n")
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + rtNormFactors <- getRTNormFactors(esetTmp, minFeaturesPerBin=100)
     + stopifnot(nrow(rtNormalize(esetTmp,rtNormFactors)) == 97)
     +
     + # Stop if rtNormFactors doesn't cover all retention times.
     + #rtNormalize(esetTmp,rtNormFactors[1:2,])
     +
     + cat(" --- testRTNormalize: PASS ALL TEST --- \n")
     + }
     >
     > testRemoveOutliers <- function(){
     +
     + cat(" --- testRemoveOutliers --- \n")
     + set.seed(1234)
     + stopifnot(sum(is.na(removeOutliers(c(-10, rnorm(100), 10)))) == 2)
     + cat(" --- testRemoveOutliers: PASS ALL TEST --- \n")
     + }
     >
     > testPerFeatureNormalization <- function(){
     +
     + cat(" --- testPerFeatureNormalization: --- \n")
     +
     + normFactors <- exprs(eset)[1:10,1:3]
     + colnames(normFactors) <- c("A","B","C")
     + rownames(normFactors) <- fData(eset)[1:10,]$proteinName
     + normFactors[is.finite(normFactors)] <- 1
     + eNorm <- perFeatureNormalization(eset,normFactors)
     +
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,2] , (exprs(eset)[1,2]-1)))
     + stopifnot(all.equal(exprs(eNorm)[13,2] , (exprs(eset)[13,2])))
     +
     + normFactors[,2] <- 200
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,3] , (exprs(eset)[1,3]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,4] , (exprs(eset)[1,4]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,5] , (exprs(eset)[1,5]-1)))
     +
     + normFactors[,3] <- 0
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,5] , exprs(eset)[1,5]))
     + stopifnot(all.equal(exprs(eNorm)[2,6] , exprs(eset)[2,6]))
     +
     + normFactors[3,] <- 1000
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + # re-order normFactors columns
     + eNorm <- perFeatureNormalization(eset,normFactors[,rev(colnames(normFactors))])
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + cat(" --- testPerFeatureNormalization: PASS ALL TEST --- \n")
     +
     + #coveredPeptideSel <- fData(eset)$proteinName %in% rownames(normFactors)
     + #exprs(eset)[coveredPeptideSel,] <- exprs(eset)[coveredPeptideSel, ] - normFactors[as.character(fData(eset)[coveredPeptideSel,]$proteinName),pData(eset)$condition]
     +
     + }
     >
     >
     > testStandardise <- function(){
     +
     + cat(" --- testStandardise: --- \n")
     +
     + d <- data.frame(rnorm(10000,5,20), rnorm(10000,10,10))
     + dStd <- standardise(d[,1])
     +
     + stopifnot(round(mean(dStd)) == 0 )
     + stopifnot(round(sd(dStd)) == 1 )
     +
     + dStd <- standardise(d)
     + stopifnot(round(apply(dStd,2,mean)[1]) == 0)
     + stopifnot(round(apply(dStd,2,sd)[1]) == 1)
     +
     + cat(" --- testStandardise: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetMaxIndex <-function(){
     +
     + cat(" --- testGetMaxIndex: --- \n")
     + d <- data.frame(s=c(NA,NA,NA,NA,1,1:4),lab=sort(rep(c("A","B","C"),3)))
     + DT <- data.table(d)
     + setkey(DT,lab)
     +
     +
     + stopifnot(all.equal(c(1,5,9) , DT[, .I[getMaxIndex(s)], by=lab ]$V1 ))
     + cat(" --- testGetMaxIndex: PASS ALL TEST --- \n")
     +
     + }
     >
     > testCreatePairedExpDesign <- function(){
     +
     + cat(" --- testCreatePairedExpDesign: --- \n")
     + stopifnot(all( pData(createPairedExpDesign(eset))$subject == as.factor(rep(1:2,3))))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:3]), silent = TRUE), "try-error")))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:4]), silent = TRUE), "ExpressionSet")))
     + cat(" --- testCreatePairedExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     > ### TEST FUNCTIONS END
     >
     > #### TESTS
     > #testGetRatios()
     > #testGetAllEBayes()
     > #testGetSignalPerCondition()
     > #testGetRatios()
     >
     > if(T){
     + testCreateExpressionDataset()
     + testGetAllEBayes()
     + testGetRatios()
     + testGetAllCV()
     + testGlobalNormalize()
     + #testNormalise()
     + testRtNormalize()
     +
     + testBaselineIntensity()
     + testRollUp()
     + testTopX()
     +
     + testGetLoocvFoldError()
     +
     + testRemoveOutliers()
     + testPerFeatureNormalization()
     + testStandardise()
     + testGetMaxIndex()
     +
     + testGetIBAQEset()
     +
     + testCreatePairedExpDesign()
     +
     + }
     --- testCreateExpressionDataset: ---
     Error in testCreateExpressionDataset() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testCreateExpressionDataset -> stopifnot
     Execution halted
    Running the tests in ‘tests/testUserOptions.R’ failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     >
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testExpDesignTagToExpDesign <- function(){
     +
     + cat("--- testExpDesignTagToExpDesign: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     +
     + expDesignString1 <- "1,2,3:4,5,6"
     +
     + # 6-plex default: 1,2,3:4,5,6
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 1 TRUE
     + #3 Condition 1 TRUE
     + #4 Condition 2 FALSE
     + #5 Condition 2 FALSE
     + #6 Condition 2 FALSE
     +
     +
     + expDesign <- data.frame(condition=paste("Condition",sort(rep(c(1,2),3))),isControl=sort(rep(c(T,F),3),decreasing=T) )
     +
     + expDesign1 <- expDesignTagToExpDesign(expDesignString1, expDesign)
     +
     + stopifnot(nrow(expDesign1) == 6 )
     + stopifnot(length(unique(expDesign1$condition)) == 2 )
     + stopifnot(sum(expDesign1$isControl) == 3 )
     +
     + expDesignString2 <- "1,4,7,10:2,5,8:3,6,9"
     +
     + # 10-plex default is "1,4,7,10:2,5,8:3,6,9"
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 2 FALSE
     + #3 Condition 3 FALSE
     + #4 Condition 1 TRUE
     + #5 Condition 2 FALSE
     + #6 Condition 3 FALSE
     + #7 Condition 1 TRUE
     + #8 Condition 2 FALSE
     + #9 Condition 3 FALSE
     + #10 Condition 1 TRUE
     +
     + expDesign <- data.frame(condition=paste("Condition",c(1,2,3,1,2,3,1,2,3,1)),isControl=c(T,F,F,T,F,F,T,F,F,T) )
     + expDesign2 <- expDesignTagToExpDesign(expDesignString2, expDesign)
     + stopifnot(nrow(expDesign2) == 10 )
     + stopifnot(length(unique(expDesign2$condition)) == 3 )
     + stopifnot(sum(expDesign2$isControl) == 4 )
     +
     + ### condition name assignment when mixing runs from different conditions
     + expDesign <- data.frame(condition=paste("foo",c(1,1,1,2,2,3,3)),isControl=c(F,F,F,T,T,F,F) )
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5:6",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1:4,6:5",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1,2,4",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("2",expDesign)$condition)))
     + stopifnot( length(unique(expDesignTagToExpDesign("1:2:3:4:5:6",expDesign)$condition)) == 6)
     +
     + cat("--- testExpDesignTagToExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > ### TEST FUNCTIONS END
     >
     > ### TESTS
     > testExpDesignTagToExpDesign()
     --- testExpDesignTagToExpDesign: ---
     Error in testExpDesignTagToExpDesign() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testExpDesignTagToExpDesign -> stopifnot
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.3.1
Check: tests
Result: ERROR
     Running ‘initTestSession.R’ [17s/21s]
     Running ‘runAllTest.R’
     Running ‘testExpressionAnalysis.R’ [17s/21s]
     Running ‘testGraphics.R’ [27s/34s]
     Running ‘testIdentificationAnalysis.R’ [18s/21s]
     Running ‘testParser.R’ [19s/23s]
     Running ‘testSafeQuantAnalysis.R’ [25s/31s]
     Running ‘testTMT.R’ [17s/20s]
     Running ‘testUserOptions.R’ [17s/22s]
    Running the tests in ‘tests/testExpressionAnalysis.R’ failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testCreateExpressionDataset <- function(){
     +
     + cat("--- testCreateExpressionDataset: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     + cat("--- testCreateExpressionDataset: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > testGetAllEBayes <- function(){
     +
     +
     + cat("--- testGetAllEBayes: --- \n")
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + pAdj <- getAllEBayes(eset, adjust=T)
     +
     + stopifnot( mean(pAdj[,"A"]) > mean(p[,"A"]) )
     +
     + ### paired desgn
     + esetNonPaired <- esetPaired
     + pData(esetNonPaired) <- pData(esetPaired)[,1:2]
     +
     + pValPaired <- getAllEBayes(esetPaired,adjust=F,method=c("all"))
     + pValPairedPairwise <- getAllEBayes(esetPaired,adjust=F,method=c("pairwise"))
     +
     + pValNonPaired <- getAllEBayes(esetNonPaired,adjust=F,method=c("all"))
     + pValNonPairedPairwise <- getAllEBayes(esetNonPaired,adjust=F,method=c("pairwise"))
     + stopifnot(all(apply(pValPaired,2,sum) < apply(pValNonPaired,2,sum)))
     + stopifnot(all(apply(pValPairedPairwise,2,sum) < apply(pValNonPairedPairwise,2,sum)))
     +
     + # adjustment filter
     +
     + adjustfilter <- data.frame(rep(T,nrow(eset)),rep(T,nrow(eset)) )
     + adjustfilter[1,1] <- F
     + adjustfilter[2,2] <- F
     +
     + pTmp <- getAllEBayes(eset,adjust=T, adjustFilter=adjustfilter)
     + stopifnot(p[1,1] == pTmp[1,1])
     + stopifnot(p[2,2] == pTmp[2,2])
     + stopifnot(is.na(pTmp[3,2]))
     + cat("--- testGetAllEBayes: PASS ALL TEST --- \n")
     +
     + # Question: limma multiple groups comparison produces different pvalue comparing with two group comparsion
     + # https://support.bioconductor.org/p/44216/
     + # https://support.bioconductor.org/p/60556/
     + }
     >
     > testGetRatios <- function(){
     +
     + cat("--- testGetRatios: --- \n")
     +
     + r <- getRatios(eset)
     +
     + exprs(eset)[1,c(5:6,1:2)]
     + # C_rep_1 C_rep_2 A_rep_1 A_rep_2
     + # 9.963852 9.966003 9.965568 9.967214
     +
     + ## NOTE: C is control
     + stopifnot(all.equal(r[1,1],median(log2(exprs(eset))[1,1:2]) - median(log2(exprs(eset))[1,5:6]) ) )
     +
     + stopifnot(mean(r[,"A"]) < mean(r[,"B"]))
     + stopifnot(all.equal(r,getRatios(eset,method="mean")))
     + r <- getRatios(eset)
     + stopifnot(all.equal(mean(r[,"B"]),mean(r[,"B"])))
     +
     + stopifnot(all(round(apply(getRatios(esetPaired, log2=F),2,mean),1) == c(1.5,1.2)))
     + stopifnot(ncol(r) == 2)
     +
     + rPaired <- getRatios(esetPaired, method="paired")
     + stopifnot(ncol(rPaired) == 4)
     + stopifnot(all( log2(exprs(esetPaired)[,1]) - log2(exprs(esetPaired)[,5]) == rPaired[,1] ))
     + stopifnot(all( log2(exprs(esetPaired)[,4]) - log2(exprs(esetPaired)[,6]) == rPaired[,4] ))
     + stopifnot(all( exprs(esetPaired)[,4] / exprs(esetPaired)[,6] == getRatios(esetPaired, method="paired", log2=F)[,4] ))
     + # should fail
     + stopifnot((inherits(try( getRatios(eset, method="paired"), silent = TRUE), "try-error")))
     +
     +
     + stopifnot(all(round(getRatios(esetPaired)[,1],2) == round(apply(rPaired[,1:2],1,median),2)))
     +
     +
     + cat("--- testGetRatios: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetAllCV <- function(){
     +
     + cat("--- testGetAllCV: --- \n")
     +
     + cv <- getAllCV(eset)
     +
     + stopifnot(all.equal(cv[1,"A"] , (sd(exprs(eset)[1,unlist(pData(eset)$condition == "A")]) / mean(exprs(eset)[1,unlist(pData(eset)$condition == "A")]))))
     + stopifnot(all.equal(cv[200,"C"] , sd(exprs(eset)[200,unlist(pData(eset)$condition == "C")]) / mean(exprs(eset)[200,unlist(pData(eset)$condition == "C")])))
     +
     + cvPaired <- getAllCV(esetPaired)
     + stopifnot(all(is.na(cvPaired[,1])))
     + stopifnot(all(!is.na(cvPaired[,2])))
     + stopifnot(cvPaired[3,"A"] == (sd(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6]) / mean(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6])))
     +
     + cat("--- testGetAllCV: PASS ALL TEST --- \n")
     + }
     >
     > testGlobalNormalize <- function(){
     +
     + cat("--- testGlobalNormalize: --- \n")
     +
     + globalNormFactors <- getGlobalNormFactors(eset,method="sum")
     + ### add normalization factors to ExpressionSet
     + pData(eset) <- cbind(pData(eset),globalNormFactors)
     + esetNorm <- globalNormalize(eset,globalNormFactors)
     +
     + stopifnot(all.equal(as.vector(unlist(apply(exprs(esetNorm),2,sum))),as.vector(rev(unlist(apply(exprs(esetNorm),2,sum))))))
     +
     + stopifnot(pData(esetNorm)$normFactor[1] == 1)
     + stopifnot(pData(esetNorm)$normFactor[2] != 1)
     +
     + cat("--- testGlobalNormalize: PASS ALL TEST --- \n")
     +
     + # Should generate error and stop
     + # fData(eset)$isNormAnchor <- rep(F,nrow(eset))
     + # esetNorm <- normalizeIntensities(eset)
     +
     + }
     >
     > testGetSignalPerCondition <- function(){
     +
     + cat("--- testGetSignalPerCondition: --- \n")
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"A"] <= getSignalPerCondition(eset,method="max")[,"A"]) == nrow(eset))
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"C"] <= getSignalPerCondition(eset,method="median")[,"C"]) == nrow(eset))
     + stopifnot(getSignalPerCondition(eset,method="sd")[1,2] == sd(exprs(eset)[1,3:4]))
     + cat("--- testGetSignalPerCondition: PASS ALL TEST --- \n")
     + }
     >
     > testBaselineIntensity <- function(){
     +
     + cat("--- testBaselineIntensity: --- \n")
     +
     + allInt <- as.vector(unlist(exprs(eset)))
     + bl <- round(getBaselineIntensity(allInt,promille=5),2)
     + #hist(allInt)
     + #abline(v=bl,lwd=2)
     + stopifnot(all.equal(bl[[1]] , 997.82) )
     +
     +
     + set.seed(1234)
     + suppressWarnings(allInt2 <- log10(rnorm(1000,1,1)))
     + bl2 <- round(getBaselineIntensity(allInt2,promille=5),2)
     + stopifnot(all.equal(-1.95,bl2[[1]]))
     + #hist(allInt2)
     + #abline(v=bl2,lwd=2)
     +
     + cat("--- testBaselineIntensity: PASS ALL TEST --- \n")
     +
     + }
     >
     > testRollUp <- function(){
     +
     + cat(" --- testRollUp --- \n")
     +
     + rollUpEset1 <- rollUp(eset,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$proteinName ) ) == nrow(rollUpEset1))
     +
     + rollUpEset2 <- rollUp(eset ,featureDataColumnName= c("ptm"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset2))
     +
     + rollUpEset3 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("ptm"), method=c("mean"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset3))
     +
     + #print(exprs(rollUpEset2))
     +
     + stopifnot(all.equal(sum(exprs(rollUpEset2)),sum(exprs(rollUpEset1)))) ### test sum
     + stopifnot(sum(exprs(rollUpEset1)) != sum(exprs(rollUpEset3))) ### test mean
     +
     + rollUpEset4 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))
     + stopifnot(sum(exprs(rollUpEset3)) != sum(exprs(rollUpEset4)) ) ### test top 3
     +
     + cat(" --- testRollUp: PASS ALL TEST --- \n")
     +
     + # progenesisFeatureCsvFile3 <- "/Users/ahrnee-adm/dev/R/workspace/SafeQuant/inst/testData/2014/peptides2.csv"
     + # d <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile3,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile3))
     + # system.time(e <- rollUp(d, method="sum", isProgressBar=T, featureDataColumnName= c("peptide")))
     + # system.time(e <- rollUpDT(d, method="sum", featureDataColumnName= c("peptide")))
     + #
     + esetTmp <- parseProgenesisPeptideMeasurementCsv(progenesisPeptideMeasurementCsvFile1,expDesign= getExpDesignProgenesisCsv(progenesisPeptideMeasurementCsvFile1))
     +
     + fData(esetTmp)
     +
     + rollUpEsetProteinAllAccessions <- rollUp(esetTmp,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot(fData(rollUpEsetProteinAllAccessions)$allAccessionsTMP[68] == "sp|E9PAV3|NACAM_HUMAN;sp|Q9BZK3|NACP1_HUMAN")
     +
     + }
     >
     > testTopX <- function(){
     +
     + cat(" --- testTopX --- \n")
     +
     + entryData1 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,5),ncol=4)))
     + rownames(entryData1) <- paste("peptide",1:nrow(entryData1),sep="_")
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 5
     + stopifnot(all.equal(rep(10/3,3) , as.vector(unlist(getTopX(entryData1))) ))
     +
     + entryData2 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,NA),ncol=4)))
     + rownames(entryData2) <- paste("peptide",1:nrow(entryData2),sep="_")
     +
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 NA
     + stopifnot(all.equal(c(4,4,3) , as.vector(unlist(getTopX(entryData2,topX=2)))))
     +
     + # 1 row
     + stopifnot(all.equal(rep(1,3),as.vector(unlist(getTopX(entryData1[1,])))))
     +
     + # 1 col
     + stopifnot(all.equal(getTopX(entryData1)[[1]],getTopX(entryData1[,1])))
     +
     + top1 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top1"))),1,sum)
     + top3 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))),1,sum)
     + meanInt <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("mean"))),1,sum)
     +
     + stopifnot(sum(top1 >= top3 ) == length(top3))
     + stopifnot(sum(top1) > sum(top3))
     + stopifnot(sum(top1) > sum(meanInt))
     + stopifnot(all.equal(sum(top3),sum(meanInt)))
     +
     + cat(" --- testTopX: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetIBAQEset <- function(){
     +
     + cat(" --- testGetIBAQEset --- \n")
     +
     + # read protein fasta
     + proteinDB <- read.fasta(fastaFile,seqtype = "AA",as.string = TRUE, set.attributes = FALSE)
     +
     + iBaqEset <- getIBAQEset(eset,proteinDB=proteinDB)
     + stopifnot(round(exprs(iBaqEset))[1,1] == 125)
     + stopifnot(round(exprs(iBaqEset))[2,2] == 38)
     +
     + cat(" --- testGetIBAQEset: PASS ALL TEST --- \n")
     + }
     >
     >
     > testGetLoocvFoldError <- function(){
     +
     + cat(" --- testGetLoocvFoldError --- \n")
     + #plotCalibrationCurve(fit)
     + stopifnot( round(sum(getLoocvFoldError(absEstSimData))) == -8)
     + cat(" --- testGetLoocvFoldError: PASS ALL TEST --- \n")
     + }
     >
     > testSqNormalize <- function(){
     +
     + cat(" --- testSqNormalize --- \n")
     +
     + stopifnot(nrow(sqNormalize(eset, method = "global")) == 900)
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + stopifnot(nrow(sqNormalize(esetTmp, method = "rt")) == 496)
     +
     + cat(" --- testSqNormalize: PASS ALL TEST --- \n")
     + }
     >
     >
     > testRtNormalize <- function(){
     +
     +
     + cat(" --- testRTNormalize --- \n")
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + rtNormFactors <- getRTNormFactors(esetTmp, minFeaturesPerBin=100)
     + stopifnot(nrow(rtNormalize(esetTmp,rtNormFactors)) == 97)
     +
     + # Stop if rtNormFactors doesn't cover all retention times.
     + #rtNormalize(esetTmp,rtNormFactors[1:2,])
     +
     + cat(" --- testRTNormalize: PASS ALL TEST --- \n")
     + }
     >
     > testRemoveOutliers <- function(){
     +
     + cat(" --- testRemoveOutliers --- \n")
     + set.seed(1234)
     + stopifnot(sum(is.na(removeOutliers(c(-10, rnorm(100), 10)))) == 2)
     + cat(" --- testRemoveOutliers: PASS ALL TEST --- \n")
     + }
     >
     > testPerFeatureNormalization <- function(){
     +
     + cat(" --- testPerFeatureNormalization: --- \n")
     +
     + normFactors <- exprs(eset)[1:10,1:3]
     + colnames(normFactors) <- c("A","B","C")
     + rownames(normFactors) <- fData(eset)[1:10,]$proteinName
     + normFactors[is.finite(normFactors)] <- 1
     + eNorm <- perFeatureNormalization(eset,normFactors)
     +
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,2] , (exprs(eset)[1,2]-1)))
     + stopifnot(all.equal(exprs(eNorm)[13,2] , (exprs(eset)[13,2])))
     +
     + normFactors[,2] <- 200
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,3] , (exprs(eset)[1,3]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,4] , (exprs(eset)[1,4]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,5] , (exprs(eset)[1,5]-1)))
     +
     + normFactors[,3] <- 0
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,5] , exprs(eset)[1,5]))
     + stopifnot(all.equal(exprs(eNorm)[2,6] , exprs(eset)[2,6]))
     +
     + normFactors[3,] <- 1000
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + # re-order normFactors columns
     + eNorm <- perFeatureNormalization(eset,normFactors[,rev(colnames(normFactors))])
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + cat(" --- testPerFeatureNormalization: PASS ALL TEST --- \n")
     +
     + #coveredPeptideSel <- fData(eset)$proteinName %in% rownames(normFactors)
     + #exprs(eset)[coveredPeptideSel,] <- exprs(eset)[coveredPeptideSel, ] - normFactors[as.character(fData(eset)[coveredPeptideSel,]$proteinName),pData(eset)$condition]
     +
     + }
     >
     >
     > testStandardise <- function(){
     +
     + cat(" --- testStandardise: --- \n")
     +
     + d <- data.frame(rnorm(10000,5,20), rnorm(10000,10,10))
     + dStd <- standardise(d[,1])
     +
     + stopifnot(round(mean(dStd)) == 0 )
     + stopifnot(round(sd(dStd)) == 1 )
     +
     + dStd <- standardise(d)
     + stopifnot(round(apply(dStd,2,mean)[1]) == 0)
     + stopifnot(round(apply(dStd,2,sd)[1]) == 1)
     +
     + cat(" --- testStandardise: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetMaxIndex <-function(){
     +
     + cat(" --- testGetMaxIndex: --- \n")
     + d <- data.frame(s=c(NA,NA,NA,NA,1,1:4),lab=sort(rep(c("A","B","C"),3)))
     + DT <- data.table(d)
     + setkey(DT,lab)
     +
     +
     + stopifnot(all.equal(c(1,5,9) , DT[, .I[getMaxIndex(s)], by=lab ]$V1 ))
     + cat(" --- testGetMaxIndex: PASS ALL TEST --- \n")
     +
     + }
     >
     > testCreatePairedExpDesign <- function(){
     +
     + cat(" --- testCreatePairedExpDesign: --- \n")
     + stopifnot(all( pData(createPairedExpDesign(eset))$subject == as.factor(rep(1:2,3))))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:3]), silent = TRUE), "try-error")))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:4]), silent = TRUE), "ExpressionSet")))
     + cat(" --- testCreatePairedExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     > ### TEST FUNCTIONS END
     >
     > #### TESTS
     > #testGetRatios()
     > #testGetAllEBayes()
     > #testGetSignalPerCondition()
     > #testGetRatios()
     >
     > if(T){
     + testCreateExpressionDataset()
     + testGetAllEBayes()
     + testGetRatios()
     + testGetAllCV()
     + testGlobalNormalize()
     + #testNormalise()
     + testRtNormalize()
     +
     + testBaselineIntensity()
     + testRollUp()
     + testTopX()
     +
     + testGetLoocvFoldError()
     +
     + testRemoveOutliers()
     + testPerFeatureNormalization()
     + testStandardise()
     + testGetMaxIndex()
     +
     + testGetIBAQEset()
     +
     + testCreatePairedExpDesign()
     +
     + }
     --- testCreateExpressionDataset: ---
     Error in testCreateExpressionDataset() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testCreateExpressionDataset -> stopifnot
     Execution halted
    Running the tests in ‘tests/testUserOptions.R’ failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     >
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testExpDesignTagToExpDesign <- function(){
     +
     + cat("--- testExpDesignTagToExpDesign: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     +
     + expDesignString1 <- "1,2,3:4,5,6"
     +
     + # 6-plex default: 1,2,3:4,5,6
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 1 TRUE
     + #3 Condition 1 TRUE
     + #4 Condition 2 FALSE
     + #5 Condition 2 FALSE
     + #6 Condition 2 FALSE
     +
     +
     + expDesign <- data.frame(condition=paste("Condition",sort(rep(c(1,2),3))),isControl=sort(rep(c(T,F),3),decreasing=T) )
     +
     + expDesign1 <- expDesignTagToExpDesign(expDesignString1, expDesign)
     +
     + stopifnot(nrow(expDesign1) == 6 )
     + stopifnot(length(unique(expDesign1$condition)) == 2 )
     + stopifnot(sum(expDesign1$isControl) == 3 )
     +
     + expDesignString2 <- "1,4,7,10:2,5,8:3,6,9"
     +
     + # 10-plex default is "1,4,7,10:2,5,8:3,6,9"
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 2 FALSE
     + #3 Condition 3 FALSE
     + #4 Condition 1 TRUE
     + #5 Condition 2 FALSE
     + #6 Condition 3 FALSE
     + #7 Condition 1 TRUE
     + #8 Condition 2 FALSE
     + #9 Condition 3 FALSE
     + #10 Condition 1 TRUE
     +
     + expDesign <- data.frame(condition=paste("Condition",c(1,2,3,1,2,3,1,2,3,1)),isControl=c(T,F,F,T,F,F,T,F,F,T) )
     + expDesign2 <- expDesignTagToExpDesign(expDesignString2, expDesign)
     + stopifnot(nrow(expDesign2) == 10 )
     + stopifnot(length(unique(expDesign2$condition)) == 3 )
     + stopifnot(sum(expDesign2$isControl) == 4 )
     +
     + ### condition name assignment when mixing runs from different conditions
     + expDesign <- data.frame(condition=paste("foo",c(1,1,1,2,2,3,3)),isControl=c(F,F,F,T,T,F,F) )
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5:6",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1:4,6:5",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1,2,4",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("2",expDesign)$condition)))
     + stopifnot( length(unique(expDesignTagToExpDesign("1:2:3:4:5:6",expDesign)$condition)) == 6)
     +
     + cat("--- testExpDesignTagToExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > ### TEST FUNCTIONS END
     >
     > ### TESTS
     > testExpDesignTagToExpDesign()
     --- testExpDesignTagToExpDesign: ---
     Error in testExpDesignTagToExpDesign() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testExpDesignTagToExpDesign -> stopifnot
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.3.1
Check: tests
Result: ERROR
     Running ‘initTestSession.R’ [17s/22s]
     Running ‘runAllTest.R’
     Running ‘testExpressionAnalysis.R’ [18s/23s]
     Running ‘testGraphics.R’ [28s/34s]
     Running ‘testIdentificationAnalysis.R’ [20s/27s]
     Running ‘testParser.R’ [20s/24s]
     Running ‘testSafeQuantAnalysis.R’ [25s/30s]
     Running ‘testTMT.R’ [17s/21s]
     Running ‘testUserOptions.R’ [18s/24s]
    Running the tests in ‘tests/testExpressionAnalysis.R’ failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testCreateExpressionDataset <- function(){
     +
     + cat("--- testCreateExpressionDataset: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     + cat("--- testCreateExpressionDataset: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > testGetAllEBayes <- function(){
     +
     +
     + cat("--- testGetAllEBayes: --- \n")
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + pAdj <- getAllEBayes(eset, adjust=T)
     +
     + stopifnot( mean(pAdj[,"A"]) > mean(p[,"A"]) )
     +
     + ### paired desgn
     + esetNonPaired <- esetPaired
     + pData(esetNonPaired) <- pData(esetPaired)[,1:2]
     +
     + pValPaired <- getAllEBayes(esetPaired,adjust=F,method=c("all"))
     + pValPairedPairwise <- getAllEBayes(esetPaired,adjust=F,method=c("pairwise"))
     +
     + pValNonPaired <- getAllEBayes(esetNonPaired,adjust=F,method=c("all"))
     + pValNonPairedPairwise <- getAllEBayes(esetNonPaired,adjust=F,method=c("pairwise"))
     + stopifnot(all(apply(pValPaired,2,sum) < apply(pValNonPaired,2,sum)))
     + stopifnot(all(apply(pValPairedPairwise,2,sum) < apply(pValNonPairedPairwise,2,sum)))
     +
     + # adjustment filter
     +
     + adjustfilter <- data.frame(rep(T,nrow(eset)),rep(T,nrow(eset)) )
     + adjustfilter[1,1] <- F
     + adjustfilter[2,2] <- F
     +
     + pTmp <- getAllEBayes(eset,adjust=T, adjustFilter=adjustfilter)
     + stopifnot(p[1,1] == pTmp[1,1])
     + stopifnot(p[2,2] == pTmp[2,2])
     + stopifnot(is.na(pTmp[3,2]))
     + cat("--- testGetAllEBayes: PASS ALL TEST --- \n")
     +
     + # Question: limma multiple groups comparison produces different pvalue comparing with two group comparsion
     + # https://support.bioconductor.org/p/44216/
     + # https://support.bioconductor.org/p/60556/
     + }
     >
     > testGetRatios <- function(){
     +
     + cat("--- testGetRatios: --- \n")
     +
     + r <- getRatios(eset)
     +
     + exprs(eset)[1,c(5:6,1:2)]
     + # C_rep_1 C_rep_2 A_rep_1 A_rep_2
     + # 9.963852 9.966003 9.965568 9.967214
     +
     + ## NOTE: C is control
     + stopifnot(all.equal(r[1,1],median(log2(exprs(eset))[1,1:2]) - median(log2(exprs(eset))[1,5:6]) ) )
     +
     + stopifnot(mean(r[,"A"]) < mean(r[,"B"]))
     + stopifnot(all.equal(r,getRatios(eset,method="mean")))
     + r <- getRatios(eset)
     + stopifnot(all.equal(mean(r[,"B"]),mean(r[,"B"])))
     +
     + stopifnot(all(round(apply(getRatios(esetPaired, log2=F),2,mean),1) == c(1.5,1.2)))
     + stopifnot(ncol(r) == 2)
     +
     + rPaired <- getRatios(esetPaired, method="paired")
     + stopifnot(ncol(rPaired) == 4)
     + stopifnot(all( log2(exprs(esetPaired)[,1]) - log2(exprs(esetPaired)[,5]) == rPaired[,1] ))
     + stopifnot(all( log2(exprs(esetPaired)[,4]) - log2(exprs(esetPaired)[,6]) == rPaired[,4] ))
     + stopifnot(all( exprs(esetPaired)[,4] / exprs(esetPaired)[,6] == getRatios(esetPaired, method="paired", log2=F)[,4] ))
     + # should fail
     + stopifnot((inherits(try( getRatios(eset, method="paired"), silent = TRUE), "try-error")))
     +
     +
     + stopifnot(all(round(getRatios(esetPaired)[,1],2) == round(apply(rPaired[,1:2],1,median),2)))
     +
     +
     + cat("--- testGetRatios: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetAllCV <- function(){
     +
     + cat("--- testGetAllCV: --- \n")
     +
     + cv <- getAllCV(eset)
     +
     + stopifnot(all.equal(cv[1,"A"] , (sd(exprs(eset)[1,unlist(pData(eset)$condition == "A")]) / mean(exprs(eset)[1,unlist(pData(eset)$condition == "A")]))))
     + stopifnot(all.equal(cv[200,"C"] , sd(exprs(eset)[200,unlist(pData(eset)$condition == "C")]) / mean(exprs(eset)[200,unlist(pData(eset)$condition == "C")])))
     +
     + cvPaired <- getAllCV(esetPaired)
     + stopifnot(all(is.na(cvPaired[,1])))
     + stopifnot(all(!is.na(cvPaired[,2])))
     + stopifnot(cvPaired[3,"A"] == (sd(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6]) / mean(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6])))
     +
     + cat("--- testGetAllCV: PASS ALL TEST --- \n")
     + }
     >
     > testGlobalNormalize <- function(){
     +
     + cat("--- testGlobalNormalize: --- \n")
     +
     + globalNormFactors <- getGlobalNormFactors(eset,method="sum")
     + ### add normalization factors to ExpressionSet
     + pData(eset) <- cbind(pData(eset),globalNormFactors)
     + esetNorm <- globalNormalize(eset,globalNormFactors)
     +
     + stopifnot(all.equal(as.vector(unlist(apply(exprs(esetNorm),2,sum))),as.vector(rev(unlist(apply(exprs(esetNorm),2,sum))))))
     +
     + stopifnot(pData(esetNorm)$normFactor[1] == 1)
     + stopifnot(pData(esetNorm)$normFactor[2] != 1)
     +
     + cat("--- testGlobalNormalize: PASS ALL TEST --- \n")
     +
     + # Should generate error and stop
     + # fData(eset)$isNormAnchor <- rep(F,nrow(eset))
     + # esetNorm <- normalizeIntensities(eset)
     +
     + }
     >
     > testGetSignalPerCondition <- function(){
     +
     + cat("--- testGetSignalPerCondition: --- \n")
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"A"] <= getSignalPerCondition(eset,method="max")[,"A"]) == nrow(eset))
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"C"] <= getSignalPerCondition(eset,method="median")[,"C"]) == nrow(eset))
     + stopifnot(getSignalPerCondition(eset,method="sd")[1,2] == sd(exprs(eset)[1,3:4]))
     + cat("--- testGetSignalPerCondition: PASS ALL TEST --- \n")
     + }
     >
     > testBaselineIntensity <- function(){
     +
     + cat("--- testBaselineIntensity: --- \n")
     +
     + allInt <- as.vector(unlist(exprs(eset)))
     + bl <- round(getBaselineIntensity(allInt,promille=5),2)
     + #hist(allInt)
     + #abline(v=bl,lwd=2)
     + stopifnot(all.equal(bl[[1]] , 997.82) )
     +
     +
     + set.seed(1234)
     + suppressWarnings(allInt2 <- log10(rnorm(1000,1,1)))
     + bl2 <- round(getBaselineIntensity(allInt2,promille=5),2)
     + stopifnot(all.equal(-1.95,bl2[[1]]))
     + #hist(allInt2)
     + #abline(v=bl2,lwd=2)
     +
     + cat("--- testBaselineIntensity: PASS ALL TEST --- \n")
     +
     + }
     >
     > testRollUp <- function(){
     +
     + cat(" --- testRollUp --- \n")
     +
     + rollUpEset1 <- rollUp(eset,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$proteinName ) ) == nrow(rollUpEset1))
     +
     + rollUpEset2 <- rollUp(eset ,featureDataColumnName= c("ptm"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset2))
     +
     + rollUpEset3 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("ptm"), method=c("mean"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset3))
     +
     + #print(exprs(rollUpEset2))
     +
     + stopifnot(all.equal(sum(exprs(rollUpEset2)),sum(exprs(rollUpEset1)))) ### test sum
     + stopifnot(sum(exprs(rollUpEset1)) != sum(exprs(rollUpEset3))) ### test mean
     +
     + rollUpEset4 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))
     + stopifnot(sum(exprs(rollUpEset3)) != sum(exprs(rollUpEset4)) ) ### test top 3
     +
     + cat(" --- testRollUp: PASS ALL TEST --- \n")
     +
     + # progenesisFeatureCsvFile3 <- "/Users/ahrnee-adm/dev/R/workspace/SafeQuant/inst/testData/2014/peptides2.csv"
     + # d <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile3,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile3))
     + # system.time(e <- rollUp(d, method="sum", isProgressBar=T, featureDataColumnName= c("peptide")))
     + # system.time(e <- rollUpDT(d, method="sum", featureDataColumnName= c("peptide")))
     + #
     + esetTmp <- parseProgenesisPeptideMeasurementCsv(progenesisPeptideMeasurementCsvFile1,expDesign= getExpDesignProgenesisCsv(progenesisPeptideMeasurementCsvFile1))
     +
     + fData(esetTmp)
     +
     + rollUpEsetProteinAllAccessions <- rollUp(esetTmp,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot(fData(rollUpEsetProteinAllAccessions)$allAccessionsTMP[68] == "sp|E9PAV3|NACAM_HUMAN;sp|Q9BZK3|NACP1_HUMAN")
     +
     + }
     >
     > testTopX <- function(){
     +
     + cat(" --- testTopX --- \n")
     +
     + entryData1 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,5),ncol=4)))
     + rownames(entryData1) <- paste("peptide",1:nrow(entryData1),sep="_")
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 5
     + stopifnot(all.equal(rep(10/3,3) , as.vector(unlist(getTopX(entryData1))) ))
     +
     + entryData2 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,NA),ncol=4)))
     + rownames(entryData2) <- paste("peptide",1:nrow(entryData2),sep="_")
     +
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 NA
     + stopifnot(all.equal(c(4,4,3) , as.vector(unlist(getTopX(entryData2,topX=2)))))
     +
     + # 1 row
     + stopifnot(all.equal(rep(1,3),as.vector(unlist(getTopX(entryData1[1,])))))
     +
     + # 1 col
     + stopifnot(all.equal(getTopX(entryData1)[[1]],getTopX(entryData1[,1])))
     +
     + top1 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top1"))),1,sum)
     + top3 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))),1,sum)
     + meanInt <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("mean"))),1,sum)
     +
     + stopifnot(sum(top1 >= top3 ) == length(top3))
     + stopifnot(sum(top1) > sum(top3))
     + stopifnot(sum(top1) > sum(meanInt))
     + stopifnot(all.equal(sum(top3),sum(meanInt)))
     +
     + cat(" --- testTopX: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetIBAQEset <- function(){
     +
     + cat(" --- testGetIBAQEset --- \n")
     +
     + # read protein fasta
     + proteinDB <- read.fasta(fastaFile,seqtype = "AA",as.string = TRUE, set.attributes = FALSE)
     +
     + iBaqEset <- getIBAQEset(eset,proteinDB=proteinDB)
     + stopifnot(round(exprs(iBaqEset))[1,1] == 125)
     + stopifnot(round(exprs(iBaqEset))[2,2] == 38)
     +
     + cat(" --- testGetIBAQEset: PASS ALL TEST --- \n")
     + }
     >
     >
     > testGetLoocvFoldError <- function(){
     +
     + cat(" --- testGetLoocvFoldError --- \n")
     + #plotCalibrationCurve(fit)
     + stopifnot( round(sum(getLoocvFoldError(absEstSimData))) == -8)
     + cat(" --- testGetLoocvFoldError: PASS ALL TEST --- \n")
     + }
     >
     > testSqNormalize <- function(){
     +
     + cat(" --- testSqNormalize --- \n")
     +
     + stopifnot(nrow(sqNormalize(eset, method = "global")) == 900)
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + stopifnot(nrow(sqNormalize(esetTmp, method = "rt")) == 496)
     +
     + cat(" --- testSqNormalize: PASS ALL TEST --- \n")
     + }
     >
     >
     > testRtNormalize <- function(){
     +
     +
     + cat(" --- testRTNormalize --- \n")
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + rtNormFactors <- getRTNormFactors(esetTmp, minFeaturesPerBin=100)
     + stopifnot(nrow(rtNormalize(esetTmp,rtNormFactors)) == 97)
     +
     + # Stop if rtNormFactors doesn't cover all retention times.
     + #rtNormalize(esetTmp,rtNormFactors[1:2,])
     +
     + cat(" --- testRTNormalize: PASS ALL TEST --- \n")
     + }
     >
     > testRemoveOutliers <- function(){
     +
     + cat(" --- testRemoveOutliers --- \n")
     + set.seed(1234)
     + stopifnot(sum(is.na(removeOutliers(c(-10, rnorm(100), 10)))) == 2)
     + cat(" --- testRemoveOutliers: PASS ALL TEST --- \n")
     + }
     >
     > testPerFeatureNormalization <- function(){
     +
     + cat(" --- testPerFeatureNormalization: --- \n")
     +
     + normFactors <- exprs(eset)[1:10,1:3]
     + colnames(normFactors) <- c("A","B","C")
     + rownames(normFactors) <- fData(eset)[1:10,]$proteinName
     + normFactors[is.finite(normFactors)] <- 1
     + eNorm <- perFeatureNormalization(eset,normFactors)
     +
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,2] , (exprs(eset)[1,2]-1)))
     + stopifnot(all.equal(exprs(eNorm)[13,2] , (exprs(eset)[13,2])))
     +
     + normFactors[,2] <- 200
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,3] , (exprs(eset)[1,3]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,4] , (exprs(eset)[1,4]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,5] , (exprs(eset)[1,5]-1)))
     +
     + normFactors[,3] <- 0
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,5] , exprs(eset)[1,5]))
     + stopifnot(all.equal(exprs(eNorm)[2,6] , exprs(eset)[2,6]))
     +
     + normFactors[3,] <- 1000
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + # re-order normFactors columns
     + eNorm <- perFeatureNormalization(eset,normFactors[,rev(colnames(normFactors))])
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + cat(" --- testPerFeatureNormalization: PASS ALL TEST --- \n")
     +
     + #coveredPeptideSel <- fData(eset)$proteinName %in% rownames(normFactors)
     + #exprs(eset)[coveredPeptideSel,] <- exprs(eset)[coveredPeptideSel, ] - normFactors[as.character(fData(eset)[coveredPeptideSel,]$proteinName),pData(eset)$condition]
     +
     + }
     >
     >
     > testStandardise <- function(){
     +
     + cat(" --- testStandardise: --- \n")
     +
     + d <- data.frame(rnorm(10000,5,20), rnorm(10000,10,10))
     + dStd <- standardise(d[,1])
     +
     + stopifnot(round(mean(dStd)) == 0 )
     + stopifnot(round(sd(dStd)) == 1 )
     +
     + dStd <- standardise(d)
     + stopifnot(round(apply(dStd,2,mean)[1]) == 0)
     + stopifnot(round(apply(dStd,2,sd)[1]) == 1)
     +
     + cat(" --- testStandardise: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetMaxIndex <-function(){
     +
     + cat(" --- testGetMaxIndex: --- \n")
     + d <- data.frame(s=c(NA,NA,NA,NA,1,1:4),lab=sort(rep(c("A","B","C"),3)))
     + DT <- data.table(d)
     + setkey(DT,lab)
     +
     +
     + stopifnot(all.equal(c(1,5,9) , DT[, .I[getMaxIndex(s)], by=lab ]$V1 ))
     + cat(" --- testGetMaxIndex: PASS ALL TEST --- \n")
     +
     + }
     >
     > testCreatePairedExpDesign <- function(){
     +
     + cat(" --- testCreatePairedExpDesign: --- \n")
     + stopifnot(all( pData(createPairedExpDesign(eset))$subject == as.factor(rep(1:2,3))))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:3]), silent = TRUE), "try-error")))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:4]), silent = TRUE), "ExpressionSet")))
     + cat(" --- testCreatePairedExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     > ### TEST FUNCTIONS END
     >
     > #### TESTS
     > #testGetRatios()
     > #testGetAllEBayes()
     > #testGetSignalPerCondition()
     > #testGetRatios()
     >
     > if(T){
     + testCreateExpressionDataset()
     + testGetAllEBayes()
     + testGetRatios()
     + testGetAllCV()
     + testGlobalNormalize()
     + #testNormalise()
     + testRtNormalize()
     +
     + testBaselineIntensity()
     + testRollUp()
     + testTopX()
     +
     + testGetLoocvFoldError()
     +
     + testRemoveOutliers()
     + testPerFeatureNormalization()
     + testStandardise()
     + testGetMaxIndex()
     +
     + testGetIBAQEset()
     +
     + testCreatePairedExpDesign()
     +
     + }
     --- testCreateExpressionDataset: ---
     Error in testCreateExpressionDataset() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testCreateExpressionDataset -> stopifnot
     Execution halted
    Running the tests in ‘tests/testUserOptions.R’ failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     >
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testExpDesignTagToExpDesign <- function(){
     +
     + cat("--- testExpDesignTagToExpDesign: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     +
     + expDesignString1 <- "1,2,3:4,5,6"
     +
     + # 6-plex default: 1,2,3:4,5,6
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 1 TRUE
     + #3 Condition 1 TRUE
     + #4 Condition 2 FALSE
     + #5 Condition 2 FALSE
     + #6 Condition 2 FALSE
     +
     +
     + expDesign <- data.frame(condition=paste("Condition",sort(rep(c(1,2),3))),isControl=sort(rep(c(T,F),3),decreasing=T) )
     +
     + expDesign1 <- expDesignTagToExpDesign(expDesignString1, expDesign)
     +
     + stopifnot(nrow(expDesign1) == 6 )
     + stopifnot(length(unique(expDesign1$condition)) == 2 )
     + stopifnot(sum(expDesign1$isControl) == 3 )
     +
     + expDesignString2 <- "1,4,7,10:2,5,8:3,6,9"
     +
     + # 10-plex default is "1,4,7,10:2,5,8:3,6,9"
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 2 FALSE
     + #3 Condition 3 FALSE
     + #4 Condition 1 TRUE
     + #5 Condition 2 FALSE
     + #6 Condition 3 FALSE
     + #7 Condition 1 TRUE
     + #8 Condition 2 FALSE
     + #9 Condition 3 FALSE
     + #10 Condition 1 TRUE
     +
     + expDesign <- data.frame(condition=paste("Condition",c(1,2,3,1,2,3,1,2,3,1)),isControl=c(T,F,F,T,F,F,T,F,F,T) )
     + expDesign2 <- expDesignTagToExpDesign(expDesignString2, expDesign)
     + stopifnot(nrow(expDesign2) == 10 )
     + stopifnot(length(unique(expDesign2$condition)) == 3 )
     + stopifnot(sum(expDesign2$isControl) == 4 )
     +
     + ### condition name assignment when mixing runs from different conditions
     + expDesign <- data.frame(condition=paste("foo",c(1,1,1,2,2,3,3)),isControl=c(F,F,F,T,T,F,F) )
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5:6",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1:4,6:5",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1,2,4",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("2",expDesign)$condition)))
     + stopifnot( length(unique(expDesignTagToExpDesign("1:2:3:4:5:6",expDesign)$condition)) == 6)
     +
     + cat("--- testExpDesignTagToExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > ### TEST FUNCTIONS END
     >
     > ### TESTS
     > testExpDesignTagToExpDesign()
     --- testExpDesignTagToExpDesign: ---
     Error in testExpDesignTagToExpDesign() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testExpDesignTagToExpDesign -> stopifnot
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2.3.1
Check: tests
Result: ERROR
     Running 'initTestSession.R' [18s]
     Running 'runAllTest.R' [1s]
     Running 'testExpressionAnalysis.R' [19s]
     Running 'testGraphics.R' [28s]
     Running 'testIdentificationAnalysis.R' [20s]
     Running 'testParser.R' [21s]
     Running 'testSafeQuantAnalysis.R' [27s]
     Running 'testTMT.R' [19s]
     Running 'testUserOptions.R' [19s]
    Running the tests in 'tests/testExpressionAnalysis.R' failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testCreateExpressionDataset <- function(){
     +
     + cat("--- testCreateExpressionDataset: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     + cat("--- testCreateExpressionDataset: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > testGetAllEBayes <- function(){
     +
     +
     + cat("--- testGetAllEBayes: --- \n")
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + pAdj <- getAllEBayes(eset, adjust=T)
     +
     + stopifnot( mean(pAdj[,"A"]) > mean(p[,"A"]) )
     +
     + ### paired desgn
     + esetNonPaired <- esetPaired
     + pData(esetNonPaired) <- pData(esetPaired)[,1:2]
     +
     + pValPaired <- getAllEBayes(esetPaired,adjust=F,method=c("all"))
     + pValPairedPairwise <- getAllEBayes(esetPaired,adjust=F,method=c("pairwise"))
     +
     + pValNonPaired <- getAllEBayes(esetNonPaired,adjust=F,method=c("all"))
     + pValNonPairedPairwise <- getAllEBayes(esetNonPaired,adjust=F,method=c("pairwise"))
     + stopifnot(all(apply(pValPaired,2,sum) < apply(pValNonPaired,2,sum)))
     + stopifnot(all(apply(pValPairedPairwise,2,sum) < apply(pValNonPairedPairwise,2,sum)))
     +
     + # adjustment filter
     +
     + adjustfilter <- data.frame(rep(T,nrow(eset)),rep(T,nrow(eset)) )
     + adjustfilter[1,1] <- F
     + adjustfilter[2,2] <- F
     +
     + pTmp <- getAllEBayes(eset,adjust=T, adjustFilter=adjustfilter)
     + stopifnot(p[1,1] == pTmp[1,1])
     + stopifnot(p[2,2] == pTmp[2,2])
     + stopifnot(is.na(pTmp[3,2]))
     + cat("--- testGetAllEBayes: PASS ALL TEST --- \n")
     +
     + # Question: limma multiple groups comparison produces different pvalue comparing with two group comparsion
     + # https://support.bioconductor.org/p/44216/
     + # https://support.bioconductor.org/p/60556/
     + }
     >
     > testGetRatios <- function(){
     +
     + cat("--- testGetRatios: --- \n")
     +
     + r <- getRatios(eset)
     +
     + exprs(eset)[1,c(5:6,1:2)]
     + # C_rep_1 C_rep_2 A_rep_1 A_rep_2
     + # 9.963852 9.966003 9.965568 9.967214
     +
     + ## NOTE: C is control
     + stopifnot(all.equal(r[1,1],median(log2(exprs(eset))[1,1:2]) - median(log2(exprs(eset))[1,5:6]) ) )
     +
     + stopifnot(mean(r[,"A"]) < mean(r[,"B"]))
     + stopifnot(all.equal(r,getRatios(eset,method="mean")))
     + r <- getRatios(eset)
     + stopifnot(all.equal(mean(r[,"B"]),mean(r[,"B"])))
     +
     + stopifnot(all(round(apply(getRatios(esetPaired, log2=F),2,mean),1) == c(1.5,1.2)))
     + stopifnot(ncol(r) == 2)
     +
     + rPaired <- getRatios(esetPaired, method="paired")
     + stopifnot(ncol(rPaired) == 4)
     + stopifnot(all( log2(exprs(esetPaired)[,1]) - log2(exprs(esetPaired)[,5]) == rPaired[,1] ))
     + stopifnot(all( log2(exprs(esetPaired)[,4]) - log2(exprs(esetPaired)[,6]) == rPaired[,4] ))
     + stopifnot(all( exprs(esetPaired)[,4] / exprs(esetPaired)[,6] == getRatios(esetPaired, method="paired", log2=F)[,4] ))
     + # should fail
     + stopifnot((inherits(try( getRatios(eset, method="paired"), silent = TRUE), "try-error")))
     +
     +
     + stopifnot(all(round(getRatios(esetPaired)[,1],2) == round(apply(rPaired[,1:2],1,median),2)))
     +
     +
     + cat("--- testGetRatios: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetAllCV <- function(){
     +
     + cat("--- testGetAllCV: --- \n")
     +
     + cv <- getAllCV(eset)
     +
     + stopifnot(all.equal(cv[1,"A"] , (sd(exprs(eset)[1,unlist(pData(eset)$condition == "A")]) / mean(exprs(eset)[1,unlist(pData(eset)$condition == "A")]))))
     + stopifnot(all.equal(cv[200,"C"] , sd(exprs(eset)[200,unlist(pData(eset)$condition == "C")]) / mean(exprs(eset)[200,unlist(pData(eset)$condition == "C")])))
     +
     + cvPaired <- getAllCV(esetPaired)
     + stopifnot(all(is.na(cvPaired[,1])))
     + stopifnot(all(!is.na(cvPaired[,2])))
     + stopifnot(cvPaired[3,"A"] == (sd(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6]) / mean(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6])))
     +
     + cat("--- testGetAllCV: PASS ALL TEST --- \n")
     + }
     >
     > testGlobalNormalize <- function(){
     +
     + cat("--- testGlobalNormalize: --- \n")
     +
     + globalNormFactors <- getGlobalNormFactors(eset,method="sum")
     + ### add normalization factors to ExpressionSet
     + pData(eset) <- cbind(pData(eset),globalNormFactors)
     + esetNorm <- globalNormalize(eset,globalNormFactors)
     +
     + stopifnot(all.equal(as.vector(unlist(apply(exprs(esetNorm),2,sum))),as.vector(rev(unlist(apply(exprs(esetNorm),2,sum))))))
     +
     + stopifnot(pData(esetNorm)$normFactor[1] == 1)
     + stopifnot(pData(esetNorm)$normFactor[2] != 1)
     +
     + cat("--- testGlobalNormalize: PASS ALL TEST --- \n")
     +
     + # Should generate error and stop
     + # fData(eset)$isNormAnchor <- rep(F,nrow(eset))
     + # esetNorm <- normalizeIntensities(eset)
     +
     + }
     >
     > testGetSignalPerCondition <- function(){
     +
     + cat("--- testGetSignalPerCondition: --- \n")
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"A"] <= getSignalPerCondition(eset,method="max")[,"A"]) == nrow(eset))
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"C"] <= getSignalPerCondition(eset,method="median")[,"C"]) == nrow(eset))
     + stopifnot(getSignalPerCondition(eset,method="sd")[1,2] == sd(exprs(eset)[1,3:4]))
     + cat("--- testGetSignalPerCondition: PASS ALL TEST --- \n")
     + }
     >
     > testBaselineIntensity <- function(){
     +
     + cat("--- testBaselineIntensity: --- \n")
     +
     + allInt <- as.vector(unlist(exprs(eset)))
     + bl <- round(getBaselineIntensity(allInt,promille=5),2)
     + #hist(allInt)
     + #abline(v=bl,lwd=2)
     + stopifnot(all.equal(bl[[1]] , 997.82) )
     +
     +
     + set.seed(1234)
     + suppressWarnings(allInt2 <- log10(rnorm(1000,1,1)))
     + bl2 <- round(getBaselineIntensity(allInt2,promille=5),2)
     + stopifnot(all.equal(-1.95,bl2[[1]]))
     + #hist(allInt2)
     + #abline(v=bl2,lwd=2)
     +
     + cat("--- testBaselineIntensity: PASS ALL TEST --- \n")
     +
     + }
     >
     > testRollUp <- function(){
     +
     + cat(" --- testRollUp --- \n")
     +
     + rollUpEset1 <- rollUp(eset,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$proteinName ) ) == nrow(rollUpEset1))
     +
     + rollUpEset2 <- rollUp(eset ,featureDataColumnName= c("ptm"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset2))
     +
     + rollUpEset3 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("ptm"), method=c("mean"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset3))
     +
     + #print(exprs(rollUpEset2))
     +
     + stopifnot(all.equal(sum(exprs(rollUpEset2)),sum(exprs(rollUpEset1)))) ### test sum
     + stopifnot(sum(exprs(rollUpEset1)) != sum(exprs(rollUpEset3))) ### test mean
     +
     + rollUpEset4 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))
     + stopifnot(sum(exprs(rollUpEset3)) != sum(exprs(rollUpEset4)) ) ### test top 3
     +
     + cat(" --- testRollUp: PASS ALL TEST --- \n")
     +
     + # progenesisFeatureCsvFile3 <- "/Users/ahrnee-adm/dev/R/workspace/SafeQuant/inst/testData/2014/peptides2.csv"
     + # d <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile3,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile3))
     + # system.time(e <- rollUp(d, method="sum", isProgressBar=T, featureDataColumnName= c("peptide")))
     + # system.time(e <- rollUpDT(d, method="sum", featureDataColumnName= c("peptide")))
     + #
     + esetTmp <- parseProgenesisPeptideMeasurementCsv(progenesisPeptideMeasurementCsvFile1,expDesign= getExpDesignProgenesisCsv(progenesisPeptideMeasurementCsvFile1))
     +
     + fData(esetTmp)
     +
     + rollUpEsetProteinAllAccessions <- rollUp(esetTmp,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot(fData(rollUpEsetProteinAllAccessions)$allAccessionsTMP[68] == "sp|E9PAV3|NACAM_HUMAN;sp|Q9BZK3|NACP1_HUMAN")
     +
     + }
     >
     > testTopX <- function(){
     +
     + cat(" --- testTopX --- \n")
     +
     + entryData1 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,5),ncol=4)))
     + rownames(entryData1) <- paste("peptide",1:nrow(entryData1),sep="_")
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 5
     + stopifnot(all.equal(rep(10/3,3) , as.vector(unlist(getTopX(entryData1))) ))
     +
     + entryData2 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,NA),ncol=4)))
     + rownames(entryData2) <- paste("peptide",1:nrow(entryData2),sep="_")
     +
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 NA
     + stopifnot(all.equal(c(4,4,3) , as.vector(unlist(getTopX(entryData2,topX=2)))))
     +
     + # 1 row
     + stopifnot(all.equal(rep(1,3),as.vector(unlist(getTopX(entryData1[1,])))))
     +
     + # 1 col
     + stopifnot(all.equal(getTopX(entryData1)[[1]],getTopX(entryData1[,1])))
     +
     + top1 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top1"))),1,sum)
     + top3 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))),1,sum)
     + meanInt <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("mean"))),1,sum)
     +
     + stopifnot(sum(top1 >= top3 ) == length(top3))
     + stopifnot(sum(top1) > sum(top3))
     + stopifnot(sum(top1) > sum(meanInt))
     + stopifnot(all.equal(sum(top3),sum(meanInt)))
     +
     + cat(" --- testTopX: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetIBAQEset <- function(){
     +
     + cat(" --- testGetIBAQEset --- \n")
     +
     + # read protein fasta
     + proteinDB <- read.fasta(fastaFile,seqtype = "AA",as.string = TRUE, set.attributes = FALSE)
     +
     + iBaqEset <- getIBAQEset(eset,proteinDB=proteinDB)
     + stopifnot(round(exprs(iBaqEset))[1,1] == 125)
     + stopifnot(round(exprs(iBaqEset))[2,2] == 38)
     +
     + cat(" --- testGetIBAQEset: PASS ALL TEST --- \n")
     + }
     >
     >
     > testGetLoocvFoldError <- function(){
     +
     + cat(" --- testGetLoocvFoldError --- \n")
     + #plotCalibrationCurve(fit)
     + stopifnot( round(sum(getLoocvFoldError(absEstSimData))) == -8)
     + cat(" --- testGetLoocvFoldError: PASS ALL TEST --- \n")
     + }
     >
     > testSqNormalize <- function(){
     +
     + cat(" --- testSqNormalize --- \n")
     +
     + stopifnot(nrow(sqNormalize(eset, method = "global")) == 900)
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + stopifnot(nrow(sqNormalize(esetTmp, method = "rt")) == 496)
     +
     + cat(" --- testSqNormalize: PASS ALL TEST --- \n")
     + }
     >
     >
     > testRtNormalize <- function(){
     +
     +
     + cat(" --- testRTNormalize --- \n")
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + rtNormFactors <- getRTNormFactors(esetTmp, minFeaturesPerBin=100)
     + stopifnot(nrow(rtNormalize(esetTmp,rtNormFactors)) == 97)
     +
     + # Stop if rtNormFactors doesn't cover all retention times.
     + #rtNormalize(esetTmp,rtNormFactors[1:2,])
     +
     + cat(" --- testRTNormalize: PASS ALL TEST --- \n")
     + }
     >
     > testRemoveOutliers <- function(){
     +
     + cat(" --- testRemoveOutliers --- \n")
     + set.seed(1234)
     + stopifnot(sum(is.na(removeOutliers(c(-10, rnorm(100), 10)))) == 2)
     + cat(" --- testRemoveOutliers: PASS ALL TEST --- \n")
     + }
     >
     > testPerFeatureNormalization <- function(){
     +
     + cat(" --- testPerFeatureNormalization: --- \n")
     +
     + normFactors <- exprs(eset)[1:10,1:3]
     + colnames(normFactors) <- c("A","B","C")
     + rownames(normFactors) <- fData(eset)[1:10,]$proteinName
     + normFactors[is.finite(normFactors)] <- 1
     + eNorm <- perFeatureNormalization(eset,normFactors)
     +
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,2] , (exprs(eset)[1,2]-1)))
     + stopifnot(all.equal(exprs(eNorm)[13,2] , (exprs(eset)[13,2])))
     +
     + normFactors[,2] <- 200
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,3] , (exprs(eset)[1,3]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,4] , (exprs(eset)[1,4]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,5] , (exprs(eset)[1,5]-1)))
     +
     + normFactors[,3] <- 0
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,5] , exprs(eset)[1,5]))
     + stopifnot(all.equal(exprs(eNorm)[2,6] , exprs(eset)[2,6]))
     +
     + normFactors[3,] <- 1000
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + # re-order normFactors columns
     + eNorm <- perFeatureNormalization(eset,normFactors[,rev(colnames(normFactors))])
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + cat(" --- testPerFeatureNormalization: PASS ALL TEST --- \n")
     +
     + #coveredPeptideSel <- fData(eset)$proteinName %in% rownames(normFactors)
     + #exprs(eset)[coveredPeptideSel,] <- exprs(eset)[coveredPeptideSel, ] - normFactors[as.character(fData(eset)[coveredPeptideSel,]$proteinName),pData(eset)$condition]
     +
     + }
     >
     >
     > testStandardise <- function(){
     +
     + cat(" --- testStandardise: --- \n")
     +
     + d <- data.frame(rnorm(10000,5,20), rnorm(10000,10,10))
     + dStd <- standardise(d[,1])
     +
     + stopifnot(round(mean(dStd)) == 0 )
     + stopifnot(round(sd(dStd)) == 1 )
     +
     + dStd <- standardise(d)
     + stopifnot(round(apply(dStd,2,mean)[1]) == 0)
     + stopifnot(round(apply(dStd,2,sd)[1]) == 1)
     +
     + cat(" --- testStandardise: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetMaxIndex <-function(){
     +
     + cat(" --- testGetMaxIndex: --- \n")
     + d <- data.frame(s=c(NA,NA,NA,NA,1,1:4),lab=sort(rep(c("A","B","C"),3)))
     + DT <- data.table(d)
     + setkey(DT,lab)
     +
     +
     + stopifnot(all.equal(c(1,5,9) , DT[, .I[getMaxIndex(s)], by=lab ]$V1 ))
     + cat(" --- testGetMaxIndex: PASS ALL TEST --- \n")
     +
     + }
     >
     > testCreatePairedExpDesign <- function(){
     +
     + cat(" --- testCreatePairedExpDesign: --- \n")
     + stopifnot(all( pData(createPairedExpDesign(eset))$subject == as.factor(rep(1:2,3))))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:3]), silent = TRUE), "try-error")))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:4]), silent = TRUE), "ExpressionSet")))
     + cat(" --- testCreatePairedExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     > ### TEST FUNCTIONS END
     >
     > #### TESTS
     > #testGetRatios()
     > #testGetAllEBayes()
     > #testGetSignalPerCondition()
     > #testGetRatios()
     >
     > if(T){
     + testCreateExpressionDataset()
     + testGetAllEBayes()
     + testGetRatios()
     + testGetAllCV()
     + testGlobalNormalize()
     + #testNormalise()
     + testRtNormalize()
     +
     + testBaselineIntensity()
     + testRollUp()
     + testTopX()
     +
     + testGetLoocvFoldError()
     +
     + testRemoveOutliers()
     + testPerFeatureNormalization()
     + testStandardise()
     + testGetMaxIndex()
     +
     + testGetIBAQEset()
     +
     + testCreatePairedExpDesign()
     +
     + }
     --- testCreateExpressionDataset: ---
     Error in testCreateExpressionDataset() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testCreateExpressionDataset -> stopifnot
     Execution halted
    Running the tests in 'tests/testUserOptions.R' failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     >
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testExpDesignTagToExpDesign <- function(){
     +
     + cat("--- testExpDesignTagToExpDesign: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     +
     + expDesignString1 <- "1,2,3:4,5,6"
     +
     + # 6-plex default: 1,2,3:4,5,6
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 1 TRUE
     + #3 Condition 1 TRUE
     + #4 Condition 2 FALSE
     + #5 Condition 2 FALSE
     + #6 Condition 2 FALSE
     +
     +
     + expDesign <- data.frame(condition=paste("Condition",sort(rep(c(1,2),3))),isControl=sort(rep(c(T,F),3),decreasing=T) )
     +
     + expDesign1 <- expDesignTagToExpDesign(expDesignString1, expDesign)
     +
     + stopifnot(nrow(expDesign1) == 6 )
     + stopifnot(length(unique(expDesign1$condition)) == 2 )
     + stopifnot(sum(expDesign1$isControl) == 3 )
     +
     + expDesignString2 <- "1,4,7,10:2,5,8:3,6,9"
     +
     + # 10-plex default is "1,4,7,10:2,5,8:3,6,9"
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 2 FALSE
     + #3 Condition 3 FALSE
     + #4 Condition 1 TRUE
     + #5 Condition 2 FALSE
     + #6 Condition 3 FALSE
     + #7 Condition 1 TRUE
     + #8 Condition 2 FALSE
     + #9 Condition 3 FALSE
     + #10 Condition 1 TRUE
     +
     + expDesign <- data.frame(condition=paste("Condition",c(1,2,3,1,2,3,1,2,3,1)),isControl=c(T,F,F,T,F,F,T,F,F,T) )
     + expDesign2 <- expDesignTagToExpDesign(expDesignString2, expDesign)
     + stopifnot(nrow(expDesign2) == 10 )
     + stopifnot(length(unique(expDesign2$condition)) == 3 )
     + stopifnot(sum(expDesign2$isControl) == 4 )
     +
     + ### condition name assignment when mixing runs from different conditions
     + expDesign <- data.frame(condition=paste("foo",c(1,1,1,2,2,3,3)),isControl=c(F,F,F,T,T,F,F) )
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5:6",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1:4,6:5",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1,2,4",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("2",expDesign)$condition)))
     + stopifnot( length(unique(expDesignTagToExpDesign("1:2:3:4:5:6",expDesign)$condition)) == 6)
     +
     + cat("--- testExpDesignTagToExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > ### TEST FUNCTIONS END
     >
     > ### TESTS
     > testExpDesignTagToExpDesign()
     --- testExpDesignTagToExpDesign: ---
     Error in testExpDesignTagToExpDesign() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testExpDesignTagToExpDesign -> stopifnot
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 2.3.1
Check: tests
Result: ERROR
     Running 'initTestSession.R' [13s]
     Running 'runAllTest.R' [0s]
     Running 'testExpressionAnalysis.R' [12s]
     Running 'testGraphics.R' [21s]
     Running 'testIdentificationAnalysis.R' [13s]
     Running 'testParser.R' [18s]
     Running 'testSafeQuantAnalysis.R' [20s]
     Running 'testTMT.R' [12s]
     Running 'testUserOptions.R' [13s]
    Running the tests in 'tests/testExpressionAnalysis.R' failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testCreateExpressionDataset <- function(){
     +
     + cat("--- testCreateExpressionDataset: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     + cat("--- testCreateExpressionDataset: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > testGetAllEBayes <- function(){
     +
     +
     + cat("--- testGetAllEBayes: --- \n")
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + pAdj <- getAllEBayes(eset, adjust=T)
     +
     + stopifnot( mean(pAdj[,"A"]) > mean(p[,"A"]) )
     +
     + ### paired desgn
     + esetNonPaired <- esetPaired
     + pData(esetNonPaired) <- pData(esetPaired)[,1:2]
     +
     + pValPaired <- getAllEBayes(esetPaired,adjust=F,method=c("all"))
     + pValPairedPairwise <- getAllEBayes(esetPaired,adjust=F,method=c("pairwise"))
     +
     + pValNonPaired <- getAllEBayes(esetNonPaired,adjust=F,method=c("all"))
     + pValNonPairedPairwise <- getAllEBayes(esetNonPaired,adjust=F,method=c("pairwise"))
     + stopifnot(all(apply(pValPaired,2,sum) < apply(pValNonPaired,2,sum)))
     + stopifnot(all(apply(pValPairedPairwise,2,sum) < apply(pValNonPairedPairwise,2,sum)))
     +
     + # adjustment filter
     +
     + adjustfilter <- data.frame(rep(T,nrow(eset)),rep(T,nrow(eset)) )
     + adjustfilter[1,1] <- F
     + adjustfilter[2,2] <- F
     +
     + pTmp <- getAllEBayes(eset,adjust=T, adjustFilter=adjustfilter)
     + stopifnot(p[1,1] == pTmp[1,1])
     + stopifnot(p[2,2] == pTmp[2,2])
     + stopifnot(is.na(pTmp[3,2]))
     + cat("--- testGetAllEBayes: PASS ALL TEST --- \n")
     +
     + # Question: limma multiple groups comparison produces different pvalue comparing with two group comparsion
     + # https://support.bioconductor.org/p/44216/
     + # https://support.bioconductor.org/p/60556/
     + }
     >
     > testGetRatios <- function(){
     +
     + cat("--- testGetRatios: --- \n")
     +
     + r <- getRatios(eset)
     +
     + exprs(eset)[1,c(5:6,1:2)]
     + # C_rep_1 C_rep_2 A_rep_1 A_rep_2
     + # 9.963852 9.966003 9.965568 9.967214
     +
     + ## NOTE: C is control
     + stopifnot(all.equal(r[1,1],median(log2(exprs(eset))[1,1:2]) - median(log2(exprs(eset))[1,5:6]) ) )
     +
     + stopifnot(mean(r[,"A"]) < mean(r[,"B"]))
     + stopifnot(all.equal(r,getRatios(eset,method="mean")))
     + r <- getRatios(eset)
     + stopifnot(all.equal(mean(r[,"B"]),mean(r[,"B"])))
     +
     + stopifnot(all(round(apply(getRatios(esetPaired, log2=F),2,mean),1) == c(1.5,1.2)))
     + stopifnot(ncol(r) == 2)
     +
     + rPaired <- getRatios(esetPaired, method="paired")
     + stopifnot(ncol(rPaired) == 4)
     + stopifnot(all( log2(exprs(esetPaired)[,1]) - log2(exprs(esetPaired)[,5]) == rPaired[,1] ))
     + stopifnot(all( log2(exprs(esetPaired)[,4]) - log2(exprs(esetPaired)[,6]) == rPaired[,4] ))
     + stopifnot(all( exprs(esetPaired)[,4] / exprs(esetPaired)[,6] == getRatios(esetPaired, method="paired", log2=F)[,4] ))
     + # should fail
     + stopifnot((inherits(try( getRatios(eset, method="paired"), silent = TRUE), "try-error")))
     +
     +
     + stopifnot(all(round(getRatios(esetPaired)[,1],2) == round(apply(rPaired[,1:2],1,median),2)))
     +
     +
     + cat("--- testGetRatios: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetAllCV <- function(){
     +
     + cat("--- testGetAllCV: --- \n")
     +
     + cv <- getAllCV(eset)
     +
     + stopifnot(all.equal(cv[1,"A"] , (sd(exprs(eset)[1,unlist(pData(eset)$condition == "A")]) / mean(exprs(eset)[1,unlist(pData(eset)$condition == "A")]))))
     + stopifnot(all.equal(cv[200,"C"] , sd(exprs(eset)[200,unlist(pData(eset)$condition == "C")]) / mean(exprs(eset)[200,unlist(pData(eset)$condition == "C")])))
     +
     + cvPaired <- getAllCV(esetPaired)
     + stopifnot(all(is.na(cvPaired[,1])))
     + stopifnot(all(!is.na(cvPaired[,2])))
     + stopifnot(cvPaired[3,"A"] == (sd(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6]) / mean(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6])))
     +
     + cat("--- testGetAllCV: PASS ALL TEST --- \n")
     + }
     >
     > testGlobalNormalize <- function(){
     +
     + cat("--- testGlobalNormalize: --- \n")
     +
     + globalNormFactors <- getGlobalNormFactors(eset,method="sum")
     + ### add normalization factors to ExpressionSet
     + pData(eset) <- cbind(pData(eset),globalNormFactors)
     + esetNorm <- globalNormalize(eset,globalNormFactors)
     +
     + stopifnot(all.equal(as.vector(unlist(apply(exprs(esetNorm),2,sum))),as.vector(rev(unlist(apply(exprs(esetNorm),2,sum))))))
     +
     + stopifnot(pData(esetNorm)$normFactor[1] == 1)
     + stopifnot(pData(esetNorm)$normFactor[2] != 1)
     +
     + cat("--- testGlobalNormalize: PASS ALL TEST --- \n")
     +
     + # Should generate error and stop
     + # fData(eset)$isNormAnchor <- rep(F,nrow(eset))
     + # esetNorm <- normalizeIntensities(eset)
     +
     + }
     >
     > testGetSignalPerCondition <- function(){
     +
     + cat("--- testGetSignalPerCondition: --- \n")
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"A"] <= getSignalPerCondition(eset,method="max")[,"A"]) == nrow(eset))
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"C"] <= getSignalPerCondition(eset,method="median")[,"C"]) == nrow(eset))
     + stopifnot(getSignalPerCondition(eset,method="sd")[1,2] == sd(exprs(eset)[1,3:4]))
     + cat("--- testGetSignalPerCondition: PASS ALL TEST --- \n")
     + }
     >
     > testBaselineIntensity <- function(){
     +
     + cat("--- testBaselineIntensity: --- \n")
     +
     + allInt <- as.vector(unlist(exprs(eset)))
     + bl <- round(getBaselineIntensity(allInt,promille=5),2)
     + #hist(allInt)
     + #abline(v=bl,lwd=2)
     + stopifnot(all.equal(bl[[1]] , 997.82) )
     +
     +
     + set.seed(1234)
     + suppressWarnings(allInt2 <- log10(rnorm(1000,1,1)))
     + bl2 <- round(getBaselineIntensity(allInt2,promille=5),2)
     + stopifnot(all.equal(-1.95,bl2[[1]]))
     + #hist(allInt2)
     + #abline(v=bl2,lwd=2)
     +
     + cat("--- testBaselineIntensity: PASS ALL TEST --- \n")
     +
     + }
     >
     > testRollUp <- function(){
     +
     + cat(" --- testRollUp --- \n")
     +
     + rollUpEset1 <- rollUp(eset,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$proteinName ) ) == nrow(rollUpEset1))
     +
     + rollUpEset2 <- rollUp(eset ,featureDataColumnName= c("ptm"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset2))
     +
     + rollUpEset3 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("ptm"), method=c("mean"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset3))
     +
     + #print(exprs(rollUpEset2))
     +
     + stopifnot(all.equal(sum(exprs(rollUpEset2)),sum(exprs(rollUpEset1)))) ### test sum
     + stopifnot(sum(exprs(rollUpEset1)) != sum(exprs(rollUpEset3))) ### test mean
     +
     + rollUpEset4 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))
     + stopifnot(sum(exprs(rollUpEset3)) != sum(exprs(rollUpEset4)) ) ### test top 3
     +
     + cat(" --- testRollUp: PASS ALL TEST --- \n")
     +
     + # progenesisFeatureCsvFile3 <- "/Users/ahrnee-adm/dev/R/workspace/SafeQuant/inst/testData/2014/peptides2.csv"
     + # d <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile3,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile3))
     + # system.time(e <- rollUp(d, method="sum", isProgressBar=T, featureDataColumnName= c("peptide")))
     + # system.time(e <- rollUpDT(d, method="sum", featureDataColumnName= c("peptide")))
     + #
     + esetTmp <- parseProgenesisPeptideMeasurementCsv(progenesisPeptideMeasurementCsvFile1,expDesign= getExpDesignProgenesisCsv(progenesisPeptideMeasurementCsvFile1))
     +
     + fData(esetTmp)
     +
     + rollUpEsetProteinAllAccessions <- rollUp(esetTmp,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot(fData(rollUpEsetProteinAllAccessions)$allAccessionsTMP[68] == "sp|E9PAV3|NACAM_HUMAN;sp|Q9BZK3|NACP1_HUMAN")
     +
     + }
     >
     > testTopX <- function(){
     +
     + cat(" --- testTopX --- \n")
     +
     + entryData1 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,5),ncol=4)))
     + rownames(entryData1) <- paste("peptide",1:nrow(entryData1),sep="_")
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 5
     + stopifnot(all.equal(rep(10/3,3) , as.vector(unlist(getTopX(entryData1))) ))
     +
     + entryData2 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,NA),ncol=4)))
     + rownames(entryData2) <- paste("peptide",1:nrow(entryData2),sep="_")
     +
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 NA
     + stopifnot(all.equal(c(4,4,3) , as.vector(unlist(getTopX(entryData2,topX=2)))))
     +
     + # 1 row
     + stopifnot(all.equal(rep(1,3),as.vector(unlist(getTopX(entryData1[1,])))))
     +
     + # 1 col
     + stopifnot(all.equal(getTopX(entryData1)[[1]],getTopX(entryData1[,1])))
     +
     + top1 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top1"))),1,sum)
     + top3 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))),1,sum)
     + meanInt <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("mean"))),1,sum)
     +
     + stopifnot(sum(top1 >= top3 ) == length(top3))
     + stopifnot(sum(top1) > sum(top3))
     + stopifnot(sum(top1) > sum(meanInt))
     + stopifnot(all.equal(sum(top3),sum(meanInt)))
     +
     + cat(" --- testTopX: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetIBAQEset <- function(){
     +
     + cat(" --- testGetIBAQEset --- \n")
     +
     + # read protein fasta
     + proteinDB <- read.fasta(fastaFile,seqtype = "AA",as.string = TRUE, set.attributes = FALSE)
     +
     + iBaqEset <- getIBAQEset(eset,proteinDB=proteinDB)
     + stopifnot(round(exprs(iBaqEset))[1,1] == 125)
     + stopifnot(round(exprs(iBaqEset))[2,2] == 38)
     +
     + cat(" --- testGetIBAQEset: PASS ALL TEST --- \n")
     + }
     >
     >
     > testGetLoocvFoldError <- function(){
     +
     + cat(" --- testGetLoocvFoldError --- \n")
     + #plotCalibrationCurve(fit)
     + stopifnot( round(sum(getLoocvFoldError(absEstSimData))) == -8)
     + cat(" --- testGetLoocvFoldError: PASS ALL TEST --- \n")
     + }
     >
     > testSqNormalize <- function(){
     +
     + cat(" --- testSqNormalize --- \n")
     +
     + stopifnot(nrow(sqNormalize(eset, method = "global")) == 900)
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + stopifnot(nrow(sqNormalize(esetTmp, method = "rt")) == 496)
     +
     + cat(" --- testSqNormalize: PASS ALL TEST --- \n")
     + }
     >
     >
     > testRtNormalize <- function(){
     +
     +
     + cat(" --- testRTNormalize --- \n")
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + rtNormFactors <- getRTNormFactors(esetTmp, minFeaturesPerBin=100)
     + stopifnot(nrow(rtNormalize(esetTmp,rtNormFactors)) == 97)
     +
     + # Stop if rtNormFactors doesn't cover all retention times.
     + #rtNormalize(esetTmp,rtNormFactors[1:2,])
     +
     + cat(" --- testRTNormalize: PASS ALL TEST --- \n")
     + }
     >
     > testRemoveOutliers <- function(){
     +
     + cat(" --- testRemoveOutliers --- \n")
     + set.seed(1234)
     + stopifnot(sum(is.na(removeOutliers(c(-10, rnorm(100), 10)))) == 2)
     + cat(" --- testRemoveOutliers: PASS ALL TEST --- \n")
     + }
     >
     > testPerFeatureNormalization <- function(){
     +
     + cat(" --- testPerFeatureNormalization: --- \n")
     +
     + normFactors <- exprs(eset)[1:10,1:3]
     + colnames(normFactors) <- c("A","B","C")
     + rownames(normFactors) <- fData(eset)[1:10,]$proteinName
     + normFactors[is.finite(normFactors)] <- 1
     + eNorm <- perFeatureNormalization(eset,normFactors)
     +
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,2] , (exprs(eset)[1,2]-1)))
     + stopifnot(all.equal(exprs(eNorm)[13,2] , (exprs(eset)[13,2])))
     +
     + normFactors[,2] <- 200
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,3] , (exprs(eset)[1,3]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,4] , (exprs(eset)[1,4]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,5] , (exprs(eset)[1,5]-1)))
     +
     + normFactors[,3] <- 0
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,5] , exprs(eset)[1,5]))
     + stopifnot(all.equal(exprs(eNorm)[2,6] , exprs(eset)[2,6]))
     +
     + normFactors[3,] <- 1000
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + # re-order normFactors columns
     + eNorm <- perFeatureNormalization(eset,normFactors[,rev(colnames(normFactors))])
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + cat(" --- testPerFeatureNormalization: PASS ALL TEST --- \n")
     +
     + #coveredPeptideSel <- fData(eset)$proteinName %in% rownames(normFactors)
     + #exprs(eset)[coveredPeptideSel,] <- exprs(eset)[coveredPeptideSel, ] - normFactors[as.character(fData(eset)[coveredPeptideSel,]$proteinName),pData(eset)$condition]
     +
     + }
     >
     >
     > testStandardise <- function(){
     +
     + cat(" --- testStandardise: --- \n")
     +
     + d <- data.frame(rnorm(10000,5,20), rnorm(10000,10,10))
     + dStd <- standardise(d[,1])
     +
     + stopifnot(round(mean(dStd)) == 0 )
     + stopifnot(round(sd(dStd)) == 1 )
     +
     + dStd <- standardise(d)
     + stopifnot(round(apply(dStd,2,mean)[1]) == 0)
     + stopifnot(round(apply(dStd,2,sd)[1]) == 1)
     +
     + cat(" --- testStandardise: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetMaxIndex <-function(){
     +
     + cat(" --- testGetMaxIndex: --- \n")
     + d <- data.frame(s=c(NA,NA,NA,NA,1,1:4),lab=sort(rep(c("A","B","C"),3)))
     + DT <- data.table(d)
     + setkey(DT,lab)
     +
     +
     + stopifnot(all.equal(c(1,5,9) , DT[, .I[getMaxIndex(s)], by=lab ]$V1 ))
     + cat(" --- testGetMaxIndex: PASS ALL TEST --- \n")
     +
     + }
     >
     > testCreatePairedExpDesign <- function(){
     +
     + cat(" --- testCreatePairedExpDesign: --- \n")
     + stopifnot(all( pData(createPairedExpDesign(eset))$subject == as.factor(rep(1:2,3))))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:3]), silent = TRUE), "try-error")))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:4]), silent = TRUE), "ExpressionSet")))
     + cat(" --- testCreatePairedExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     > ### TEST FUNCTIONS END
     >
     > #### TESTS
     > #testGetRatios()
     > #testGetAllEBayes()
     > #testGetSignalPerCondition()
     > #testGetRatios()
     >
     > if(T){
     + testCreateExpressionDataset()
     + testGetAllEBayes()
     + testGetRatios()
     + testGetAllCV()
     + testGlobalNormalize()
     + #testNormalise()
     + testRtNormalize()
     +
     + testBaselineIntensity()
     + testRollUp()
     + testTopX()
     +
     + testGetLoocvFoldError()
     +
     + testRemoveOutliers()
     + testPerFeatureNormalization()
     + testStandardise()
     + testGetMaxIndex()
     +
     + testGetIBAQEset()
     +
     + testCreatePairedExpDesign()
     +
     + }
     --- testCreateExpressionDataset: ---
     Error in testCreateExpressionDataset() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testCreateExpressionDataset -> stopifnot
     Execution halted
    Running the tests in 'tests/testUserOptions.R' failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     >
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testExpDesignTagToExpDesign <- function(){
     +
     + cat("--- testExpDesignTagToExpDesign: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     +
     + expDesignString1 <- "1,2,3:4,5,6"
     +
     + # 6-plex default: 1,2,3:4,5,6
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 1 TRUE
     + #3 Condition 1 TRUE
     + #4 Condition 2 FALSE
     + #5 Condition 2 FALSE
     + #6 Condition 2 FALSE
     +
     +
     + expDesign <- data.frame(condition=paste("Condition",sort(rep(c(1,2),3))),isControl=sort(rep(c(T,F),3),decreasing=T) )
     +
     + expDesign1 <- expDesignTagToExpDesign(expDesignString1, expDesign)
     +
     + stopifnot(nrow(expDesign1) == 6 )
     + stopifnot(length(unique(expDesign1$condition)) == 2 )
     + stopifnot(sum(expDesign1$isControl) == 3 )
     +
     + expDesignString2 <- "1,4,7,10:2,5,8:3,6,9"
     +
     + # 10-plex default is "1,4,7,10:2,5,8:3,6,9"
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 2 FALSE
     + #3 Condition 3 FALSE
     + #4 Condition 1 TRUE
     + #5 Condition 2 FALSE
     + #6 Condition 3 FALSE
     + #7 Condition 1 TRUE
     + #8 Condition 2 FALSE
     + #9 Condition 3 FALSE
     + #10 Condition 1 TRUE
     +
     + expDesign <- data.frame(condition=paste("Condition",c(1,2,3,1,2,3,1,2,3,1)),isControl=c(T,F,F,T,F,F,T,F,F,T) )
     + expDesign2 <- expDesignTagToExpDesign(expDesignString2, expDesign)
     + stopifnot(nrow(expDesign2) == 10 )
     + stopifnot(length(unique(expDesign2$condition)) == 3 )
     + stopifnot(sum(expDesign2$isControl) == 4 )
     +
     + ### condition name assignment when mixing runs from different conditions
     + expDesign <- data.frame(condition=paste("foo",c(1,1,1,2,2,3,3)),isControl=c(F,F,F,T,T,F,F) )
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5:6",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1:4,6:5",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1,2,4",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("2",expDesign)$condition)))
     + stopifnot( length(unique(expDesignTagToExpDesign("1:2:3:4:5:6",expDesign)$condition)) == 6)
     +
     + cat("--- testExpDesignTagToExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > ### TEST FUNCTIONS END
     >
     > ### TESTS
     > testExpDesignTagToExpDesign()
     --- testExpDesignTagToExpDesign: ---
     Error in testExpDesignTagToExpDesign() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testExpDesignTagToExpDesign -> stopifnot
     Execution halted
Flavor: r-devel-windows-ix86+x86_64-gcc8

Version: 2.3.1
Check: tests
Result: ERROR
     Running ‘initTestSession.R’ [14s/15s]
     Running ‘runAllTest.R’ [0s/1s]
     Running ‘testExpressionAnalysis.R’ [14s/15s]
     Running ‘testGraphics.R’ [22s/27s]
     Running ‘testIdentificationAnalysis.R’ [15s/18s]
     Running ‘testParser.R’ [17s/19s]
     Running ‘testSafeQuantAnalysis.R’ [21s/24s]
     Running ‘testTMT.R’ [14s/16s]
     Running ‘testUserOptions.R’ [14s/15s]
    Running the tests in ‘tests/testExpressionAnalysis.R’ failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testCreateExpressionDataset <- function(){
     +
     + cat("--- testCreateExpressionDataset: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     + cat("--- testCreateExpressionDataset: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > testGetAllEBayes <- function(){
     +
     +
     + cat("--- testGetAllEBayes: --- \n")
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + pAdj <- getAllEBayes(eset, adjust=T)
     +
     + stopifnot( mean(pAdj[,"A"]) > mean(p[,"A"]) )
     +
     + ### paired desgn
     + esetNonPaired <- esetPaired
     + pData(esetNonPaired) <- pData(esetPaired)[,1:2]
     +
     + pValPaired <- getAllEBayes(esetPaired,adjust=F,method=c("all"))
     + pValPairedPairwise <- getAllEBayes(esetPaired,adjust=F,method=c("pairwise"))
     +
     + pValNonPaired <- getAllEBayes(esetNonPaired,adjust=F,method=c("all"))
     + pValNonPairedPairwise <- getAllEBayes(esetNonPaired,adjust=F,method=c("pairwise"))
     + stopifnot(all(apply(pValPaired,2,sum) < apply(pValNonPaired,2,sum)))
     + stopifnot(all(apply(pValPairedPairwise,2,sum) < apply(pValNonPairedPairwise,2,sum)))
     +
     + # adjustment filter
     +
     + adjustfilter <- data.frame(rep(T,nrow(eset)),rep(T,nrow(eset)) )
     + adjustfilter[1,1] <- F
     + adjustfilter[2,2] <- F
     +
     + pTmp <- getAllEBayes(eset,adjust=T, adjustFilter=adjustfilter)
     + stopifnot(p[1,1] == pTmp[1,1])
     + stopifnot(p[2,2] == pTmp[2,2])
     + stopifnot(is.na(pTmp[3,2]))
     + cat("--- testGetAllEBayes: PASS ALL TEST --- \n")
     +
     + # Question: limma multiple groups comparison produces different pvalue comparing with two group comparsion
     + # https://support.bioconductor.org/p/44216/
     + # https://support.bioconductor.org/p/60556/
     + }
     >
     > testGetRatios <- function(){
     +
     + cat("--- testGetRatios: --- \n")
     +
     + r <- getRatios(eset)
     +
     + exprs(eset)[1,c(5:6,1:2)]
     + # C_rep_1 C_rep_2 A_rep_1 A_rep_2
     + # 9.963852 9.966003 9.965568 9.967214
     +
     + ## NOTE: C is control
     + stopifnot(all.equal(r[1,1],median(log2(exprs(eset))[1,1:2]) - median(log2(exprs(eset))[1,5:6]) ) )
     +
     + stopifnot(mean(r[,"A"]) < mean(r[,"B"]))
     + stopifnot(all.equal(r,getRatios(eset,method="mean")))
     + r <- getRatios(eset)
     + stopifnot(all.equal(mean(r[,"B"]),mean(r[,"B"])))
     +
     + stopifnot(all(round(apply(getRatios(esetPaired, log2=F),2,mean),1) == c(1.5,1.2)))
     + stopifnot(ncol(r) == 2)
     +
     + rPaired <- getRatios(esetPaired, method="paired")
     + stopifnot(ncol(rPaired) == 4)
     + stopifnot(all( log2(exprs(esetPaired)[,1]) - log2(exprs(esetPaired)[,5]) == rPaired[,1] ))
     + stopifnot(all( log2(exprs(esetPaired)[,4]) - log2(exprs(esetPaired)[,6]) == rPaired[,4] ))
     + stopifnot(all( exprs(esetPaired)[,4] / exprs(esetPaired)[,6] == getRatios(esetPaired, method="paired", log2=F)[,4] ))
     + # should fail
     + stopifnot((inherits(try( getRatios(eset, method="paired"), silent = TRUE), "try-error")))
     +
     +
     + stopifnot(all(round(getRatios(esetPaired)[,1],2) == round(apply(rPaired[,1:2],1,median),2)))
     +
     +
     + cat("--- testGetRatios: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetAllCV <- function(){
     +
     + cat("--- testGetAllCV: --- \n")
     +
     + cv <- getAllCV(eset)
     +
     + stopifnot(all.equal(cv[1,"A"] , (sd(exprs(eset)[1,unlist(pData(eset)$condition == "A")]) / mean(exprs(eset)[1,unlist(pData(eset)$condition == "A")]))))
     + stopifnot(all.equal(cv[200,"C"] , sd(exprs(eset)[200,unlist(pData(eset)$condition == "C")]) / mean(exprs(eset)[200,unlist(pData(eset)$condition == "C")])))
     +
     + cvPaired <- getAllCV(esetPaired)
     + stopifnot(all(is.na(cvPaired[,1])))
     + stopifnot(all(!is.na(cvPaired[,2])))
     + stopifnot(cvPaired[3,"A"] == (sd(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6]) / mean(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6])))
     +
     + cat("--- testGetAllCV: PASS ALL TEST --- \n")
     + }
     >
     > testGlobalNormalize <- function(){
     +
     + cat("--- testGlobalNormalize: --- \n")
     +
     + globalNormFactors <- getGlobalNormFactors(eset,method="sum")
     + ### add normalization factors to ExpressionSet
     + pData(eset) <- cbind(pData(eset),globalNormFactors)
     + esetNorm <- globalNormalize(eset,globalNormFactors)
     +
     + stopifnot(all.equal(as.vector(unlist(apply(exprs(esetNorm),2,sum))),as.vector(rev(unlist(apply(exprs(esetNorm),2,sum))))))
     +
     + stopifnot(pData(esetNorm)$normFactor[1] == 1)
     + stopifnot(pData(esetNorm)$normFactor[2] != 1)
     +
     + cat("--- testGlobalNormalize: PASS ALL TEST --- \n")
     +
     + # Should generate error and stop
     + # fData(eset)$isNormAnchor <- rep(F,nrow(eset))
     + # esetNorm <- normalizeIntensities(eset)
     +
     + }
     >
     > testGetSignalPerCondition <- function(){
     +
     + cat("--- testGetSignalPerCondition: --- \n")
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"A"] <= getSignalPerCondition(eset,method="max")[,"A"]) == nrow(eset))
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"C"] <= getSignalPerCondition(eset,method="median")[,"C"]) == nrow(eset))
     + stopifnot(getSignalPerCondition(eset,method="sd")[1,2] == sd(exprs(eset)[1,3:4]))
     + cat("--- testGetSignalPerCondition: PASS ALL TEST --- \n")
     + }
     >
     > testBaselineIntensity <- function(){
     +
     + cat("--- testBaselineIntensity: --- \n")
     +
     + allInt <- as.vector(unlist(exprs(eset)))
     + bl <- round(getBaselineIntensity(allInt,promille=5),2)
     + #hist(allInt)
     + #abline(v=bl,lwd=2)
     + stopifnot(all.equal(bl[[1]] , 997.82) )
     +
     +
     + set.seed(1234)
     + suppressWarnings(allInt2 <- log10(rnorm(1000,1,1)))
     + bl2 <- round(getBaselineIntensity(allInt2,promille=5),2)
     + stopifnot(all.equal(-1.95,bl2[[1]]))
     + #hist(allInt2)
     + #abline(v=bl2,lwd=2)
     +
     + cat("--- testBaselineIntensity: PASS ALL TEST --- \n")
     +
     + }
     >
     > testRollUp <- function(){
     +
     + cat(" --- testRollUp --- \n")
     +
     + rollUpEset1 <- rollUp(eset,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$proteinName ) ) == nrow(rollUpEset1))
     +
     + rollUpEset2 <- rollUp(eset ,featureDataColumnName= c("ptm"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset2))
     +
     + rollUpEset3 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("ptm"), method=c("mean"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset3))
     +
     + #print(exprs(rollUpEset2))
     +
     + stopifnot(all.equal(sum(exprs(rollUpEset2)),sum(exprs(rollUpEset1)))) ### test sum
     + stopifnot(sum(exprs(rollUpEset1)) != sum(exprs(rollUpEset3))) ### test mean
     +
     + rollUpEset4 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))
     + stopifnot(sum(exprs(rollUpEset3)) != sum(exprs(rollUpEset4)) ) ### test top 3
     +
     + cat(" --- testRollUp: PASS ALL TEST --- \n")
     +
     + # progenesisFeatureCsvFile3 <- "/Users/ahrnee-adm/dev/R/workspace/SafeQuant/inst/testData/2014/peptides2.csv"
     + # d <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile3,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile3))
     + # system.time(e <- rollUp(d, method="sum", isProgressBar=T, featureDataColumnName= c("peptide")))
     + # system.time(e <- rollUpDT(d, method="sum", featureDataColumnName= c("peptide")))
     + #
     + esetTmp <- parseProgenesisPeptideMeasurementCsv(progenesisPeptideMeasurementCsvFile1,expDesign= getExpDesignProgenesisCsv(progenesisPeptideMeasurementCsvFile1))
     +
     + fData(esetTmp)
     +
     + rollUpEsetProteinAllAccessions <- rollUp(esetTmp,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot(fData(rollUpEsetProteinAllAccessions)$allAccessionsTMP[68] == "sp|E9PAV3|NACAM_HUMAN;sp|Q9BZK3|NACP1_HUMAN")
     +
     + }
     >
     > testTopX <- function(){
     +
     + cat(" --- testTopX --- \n")
     +
     + entryData1 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,5),ncol=4)))
     + rownames(entryData1) <- paste("peptide",1:nrow(entryData1),sep="_")
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 5
     + stopifnot(all.equal(rep(10/3,3) , as.vector(unlist(getTopX(entryData1))) ))
     +
     + entryData2 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,NA),ncol=4)))
     + rownames(entryData2) <- paste("peptide",1:nrow(entryData2),sep="_")
     +
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 NA
     + stopifnot(all.equal(c(4,4,3) , as.vector(unlist(getTopX(entryData2,topX=2)))))
     +
     + # 1 row
     + stopifnot(all.equal(rep(1,3),as.vector(unlist(getTopX(entryData1[1,])))))
     +
     + # 1 col
     + stopifnot(all.equal(getTopX(entryData1)[[1]],getTopX(entryData1[,1])))
     +
     + top1 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top1"))),1,sum)
     + top3 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))),1,sum)
     + meanInt <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("mean"))),1,sum)
     +
     + stopifnot(sum(top1 >= top3 ) == length(top3))
     + stopifnot(sum(top1) > sum(top3))
     + stopifnot(sum(top1) > sum(meanInt))
     + stopifnot(all.equal(sum(top3),sum(meanInt)))
     +
     + cat(" --- testTopX: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetIBAQEset <- function(){
     +
     + cat(" --- testGetIBAQEset --- \n")
     +
     + # read protein fasta
     + proteinDB <- read.fasta(fastaFile,seqtype = "AA",as.string = TRUE, set.attributes = FALSE)
     +
     + iBaqEset <- getIBAQEset(eset,proteinDB=proteinDB)
     + stopifnot(round(exprs(iBaqEset))[1,1] == 125)
     + stopifnot(round(exprs(iBaqEset))[2,2] == 38)
     +
     + cat(" --- testGetIBAQEset: PASS ALL TEST --- \n")
     + }
     >
     >
     > testGetLoocvFoldError <- function(){
     +
     + cat(" --- testGetLoocvFoldError --- \n")
     + #plotCalibrationCurve(fit)
     + stopifnot( round(sum(getLoocvFoldError(absEstSimData))) == -8)
     + cat(" --- testGetLoocvFoldError: PASS ALL TEST --- \n")
     + }
     >
     > testSqNormalize <- function(){
     +
     + cat(" --- testSqNormalize --- \n")
     +
     + stopifnot(nrow(sqNormalize(eset, method = "global")) == 900)
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + stopifnot(nrow(sqNormalize(esetTmp, method = "rt")) == 496)
     +
     + cat(" --- testSqNormalize: PASS ALL TEST --- \n")
     + }
     >
     >
     > testRtNormalize <- function(){
     +
     +
     + cat(" --- testRTNormalize --- \n")
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + rtNormFactors <- getRTNormFactors(esetTmp, minFeaturesPerBin=100)
     + stopifnot(nrow(rtNormalize(esetTmp,rtNormFactors)) == 97)
     +
     + # Stop if rtNormFactors doesn't cover all retention times.
     + #rtNormalize(esetTmp,rtNormFactors[1:2,])
     +
     + cat(" --- testRTNormalize: PASS ALL TEST --- \n")
     + }
     >
     > testRemoveOutliers <- function(){
     +
     + cat(" --- testRemoveOutliers --- \n")
     + set.seed(1234)
     + stopifnot(sum(is.na(removeOutliers(c(-10, rnorm(100), 10)))) == 2)
     + cat(" --- testRemoveOutliers: PASS ALL TEST --- \n")
     + }
     >
     > testPerFeatureNormalization <- function(){
     +
     + cat(" --- testPerFeatureNormalization: --- \n")
     +
     + normFactors <- exprs(eset)[1:10,1:3]
     + colnames(normFactors) <- c("A","B","C")
     + rownames(normFactors) <- fData(eset)[1:10,]$proteinName
     + normFactors[is.finite(normFactors)] <- 1
     + eNorm <- perFeatureNormalization(eset,normFactors)
     +
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,2] , (exprs(eset)[1,2]-1)))
     + stopifnot(all.equal(exprs(eNorm)[13,2] , (exprs(eset)[13,2])))
     +
     + normFactors[,2] <- 200
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,3] , (exprs(eset)[1,3]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,4] , (exprs(eset)[1,4]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,5] , (exprs(eset)[1,5]-1)))
     +
     + normFactors[,3] <- 0
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,5] , exprs(eset)[1,5]))
     + stopifnot(all.equal(exprs(eNorm)[2,6] , exprs(eset)[2,6]))
     +
     + normFactors[3,] <- 1000
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + # re-order normFactors columns
     + eNorm <- perFeatureNormalization(eset,normFactors[,rev(colnames(normFactors))])
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + cat(" --- testPerFeatureNormalization: PASS ALL TEST --- \n")
     +
     + #coveredPeptideSel <- fData(eset)$proteinName %in% rownames(normFactors)
     + #exprs(eset)[coveredPeptideSel,] <- exprs(eset)[coveredPeptideSel, ] - normFactors[as.character(fData(eset)[coveredPeptideSel,]$proteinName),pData(eset)$condition]
     +
     + }
     >
     >
     > testStandardise <- function(){
     +
     + cat(" --- testStandardise: --- \n")
     +
     + d <- data.frame(rnorm(10000,5,20), rnorm(10000,10,10))
     + dStd <- standardise(d[,1])
     +
     + stopifnot(round(mean(dStd)) == 0 )
     + stopifnot(round(sd(dStd)) == 1 )
     +
     + dStd <- standardise(d)
     + stopifnot(round(apply(dStd,2,mean)[1]) == 0)
     + stopifnot(round(apply(dStd,2,sd)[1]) == 1)
     +
     + cat(" --- testStandardise: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetMaxIndex <-function(){
     +
     + cat(" --- testGetMaxIndex: --- \n")
     + d <- data.frame(s=c(NA,NA,NA,NA,1,1:4),lab=sort(rep(c("A","B","C"),3)))
     + DT <- data.table(d)
     + setkey(DT,lab)
     +
     +
     + stopifnot(all.equal(c(1,5,9) , DT[, .I[getMaxIndex(s)], by=lab ]$V1 ))
     + cat(" --- testGetMaxIndex: PASS ALL TEST --- \n")
     +
     + }
     >
     > testCreatePairedExpDesign <- function(){
     +
     + cat(" --- testCreatePairedExpDesign: --- \n")
     + stopifnot(all( pData(createPairedExpDesign(eset))$subject == as.factor(rep(1:2,3))))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:3]), silent = TRUE), "try-error")))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:4]), silent = TRUE), "ExpressionSet")))
     + cat(" --- testCreatePairedExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     > ### TEST FUNCTIONS END
     >
     > #### TESTS
     > #testGetRatios()
     > #testGetAllEBayes()
     > #testGetSignalPerCondition()
     > #testGetRatios()
     >
     > if(T){
     + testCreateExpressionDataset()
     + testGetAllEBayes()
     + testGetRatios()
     + testGetAllCV()
     + testGlobalNormalize()
     + #testNormalise()
     + testRtNormalize()
     +
     + testBaselineIntensity()
     + testRollUp()
     + testTopX()
     +
     + testGetLoocvFoldError()
     +
     + testRemoveOutliers()
     + testPerFeatureNormalization()
     + testStandardise()
     + testGetMaxIndex()
     +
     + testGetIBAQEset()
     +
     + testCreatePairedExpDesign()
     +
     + }
     --- testCreateExpressionDataset: ---
     Error in testCreateExpressionDataset() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testCreateExpressionDataset -> stopifnot
     Execution halted
    Running the tests in ‘tests/testUserOptions.R’ failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     >
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testExpDesignTagToExpDesign <- function(){
     +
     + cat("--- testExpDesignTagToExpDesign: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     +
     + expDesignString1 <- "1,2,3:4,5,6"
     +
     + # 6-plex default: 1,2,3:4,5,6
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 1 TRUE
     + #3 Condition 1 TRUE
     + #4 Condition 2 FALSE
     + #5 Condition 2 FALSE
     + #6 Condition 2 FALSE
     +
     +
     + expDesign <- data.frame(condition=paste("Condition",sort(rep(c(1,2),3))),isControl=sort(rep(c(T,F),3),decreasing=T) )
     +
     + expDesign1 <- expDesignTagToExpDesign(expDesignString1, expDesign)
     +
     + stopifnot(nrow(expDesign1) == 6 )
     + stopifnot(length(unique(expDesign1$condition)) == 2 )
     + stopifnot(sum(expDesign1$isControl) == 3 )
     +
     + expDesignString2 <- "1,4,7,10:2,5,8:3,6,9"
     +
     + # 10-plex default is "1,4,7,10:2,5,8:3,6,9"
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 2 FALSE
     + #3 Condition 3 FALSE
     + #4 Condition 1 TRUE
     + #5 Condition 2 FALSE
     + #6 Condition 3 FALSE
     + #7 Condition 1 TRUE
     + #8 Condition 2 FALSE
     + #9 Condition 3 FALSE
     + #10 Condition 1 TRUE
     +
     + expDesign <- data.frame(condition=paste("Condition",c(1,2,3,1,2,3,1,2,3,1)),isControl=c(T,F,F,T,F,F,T,F,F,T) )
     + expDesign2 <- expDesignTagToExpDesign(expDesignString2, expDesign)
     + stopifnot(nrow(expDesign2) == 10 )
     + stopifnot(length(unique(expDesign2$condition)) == 3 )
     + stopifnot(sum(expDesign2$isControl) == 4 )
     +
     + ### condition name assignment when mixing runs from different conditions
     + expDesign <- data.frame(condition=paste("foo",c(1,1,1,2,2,3,3)),isControl=c(F,F,F,T,T,F,F) )
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5:6",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1:4,6:5",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1,2,4",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("2",expDesign)$condition)))
     + stopifnot( length(unique(expDesignTagToExpDesign("1:2:3:4:5:6",expDesign)$condition)) == 6)
     +
     + cat("--- testExpDesignTagToExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > ### TEST FUNCTIONS END
     >
     > ### TESTS
     > testExpDesignTagToExpDesign()
     --- testExpDesignTagToExpDesign: ---
     Error in testExpDesignTagToExpDesign() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testExpDesignTagToExpDesign -> stopifnot
     Execution halted
Flavor: r-patched-linux-x86_64

Version: 2.3.1
Check: tests
Result: ERROR
     Running ‘initTestSession.R’ [7s/11s]
     Running ‘runAllTest.R’ [0s/0s]
     Running ‘testExpressionAnalysis.R’ [7s/10s]
    Running the tests in ‘tests/testExpressionAnalysis.R’ failed.
    Last 13 lines of output:
     + testPerFeatureNormalization()
     + testStandardise()
     + testGetMaxIndex()
     +
     + testGetIBAQEset()
     +
     + testCreatePairedExpDesign()
     +
     + }
     --- testCreateExpressionDataset: ---
     Error in testCreateExpressionDataset() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testCreateExpressionDataset -> stopifnot
     Execution halted
Flavor: r-patched-osx-x86_64

Version: 2.3.1
Check: tests
Result: ERROR
     Running ‘initTestSession.R’ [24s/32s]
     Running ‘runAllTest.R’
     Running ‘testExpressionAnalysis.R’ [24s/34s]
     Running ‘testGraphics.R’ [39s/47s]
     Running ‘testIdentificationAnalysis.R’ [26s/39s]
     Running ‘testParser.R’ [28s/34s]
     Running ‘testSafeQuantAnalysis.R’ [35s/44s]
     Running ‘testTMT.R’ [25s/31s]
     Running ‘testUserOptions.R’ [25s/34s]
    Running the tests in ‘tests/testExpressionAnalysis.R’ failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testCreateExpressionDataset <- function(){
     +
     + cat("--- testCreateExpressionDataset: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     + cat("--- testCreateExpressionDataset: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > testGetAllEBayes <- function(){
     +
     +
     + cat("--- testGetAllEBayes: --- \n")
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + p <- getAllEBayes(eset)
     + stopifnot( mean(p[,"A"]) > mean(p[,"B"]) )
     + pAdj <- getAllEBayes(eset, adjust=T)
     +
     + stopifnot( mean(pAdj[,"A"]) > mean(p[,"A"]) )
     +
     + ### paired desgn
     + esetNonPaired <- esetPaired
     + pData(esetNonPaired) <- pData(esetPaired)[,1:2]
     +
     + pValPaired <- getAllEBayes(esetPaired,adjust=F,method=c("all"))
     + pValPairedPairwise <- getAllEBayes(esetPaired,adjust=F,method=c("pairwise"))
     +
     + pValNonPaired <- getAllEBayes(esetNonPaired,adjust=F,method=c("all"))
     + pValNonPairedPairwise <- getAllEBayes(esetNonPaired,adjust=F,method=c("pairwise"))
     + stopifnot(all(apply(pValPaired,2,sum) < apply(pValNonPaired,2,sum)))
     + stopifnot(all(apply(pValPairedPairwise,2,sum) < apply(pValNonPairedPairwise,2,sum)))
     +
     + # adjustment filter
     +
     + adjustfilter <- data.frame(rep(T,nrow(eset)),rep(T,nrow(eset)) )
     + adjustfilter[1,1] <- F
     + adjustfilter[2,2] <- F
     +
     + pTmp <- getAllEBayes(eset,adjust=T, adjustFilter=adjustfilter)
     + stopifnot(p[1,1] == pTmp[1,1])
     + stopifnot(p[2,2] == pTmp[2,2])
     + stopifnot(is.na(pTmp[3,2]))
     + cat("--- testGetAllEBayes: PASS ALL TEST --- \n")
     +
     + # Question: limma multiple groups comparison produces different pvalue comparing with two group comparsion
     + # https://support.bioconductor.org/p/44216/
     + # https://support.bioconductor.org/p/60556/
     + }
     >
     > testGetRatios <- function(){
     +
     + cat("--- testGetRatios: --- \n")
     +
     + r <- getRatios(eset)
     +
     + exprs(eset)[1,c(5:6,1:2)]
     + # C_rep_1 C_rep_2 A_rep_1 A_rep_2
     + # 9.963852 9.966003 9.965568 9.967214
     +
     + ## NOTE: C is control
     + stopifnot(all.equal(r[1,1],median(log2(exprs(eset))[1,1:2]) - median(log2(exprs(eset))[1,5:6]) ) )
     +
     + stopifnot(mean(r[,"A"]) < mean(r[,"B"]))
     + stopifnot(all.equal(r,getRatios(eset,method="mean")))
     + r <- getRatios(eset)
     + stopifnot(all.equal(mean(r[,"B"]),mean(r[,"B"])))
     +
     + stopifnot(all(round(apply(getRatios(esetPaired, log2=F),2,mean),1) == c(1.5,1.2)))
     + stopifnot(ncol(r) == 2)
     +
     + rPaired <- getRatios(esetPaired, method="paired")
     + stopifnot(ncol(rPaired) == 4)
     + stopifnot(all( log2(exprs(esetPaired)[,1]) - log2(exprs(esetPaired)[,5]) == rPaired[,1] ))
     + stopifnot(all( log2(exprs(esetPaired)[,4]) - log2(exprs(esetPaired)[,6]) == rPaired[,4] ))
     + stopifnot(all( exprs(esetPaired)[,4] / exprs(esetPaired)[,6] == getRatios(esetPaired, method="paired", log2=F)[,4] ))
     + # should fail
     + stopifnot((inherits(try( getRatios(eset, method="paired"), silent = TRUE), "try-error")))
     +
     +
     + stopifnot(all(round(getRatios(esetPaired)[,1],2) == round(apply(rPaired[,1:2],1,median),2)))
     +
     +
     + cat("--- testGetRatios: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetAllCV <- function(){
     +
     + cat("--- testGetAllCV: --- \n")
     +
     + cv <- getAllCV(eset)
     +
     + stopifnot(all.equal(cv[1,"A"] , (sd(exprs(eset)[1,unlist(pData(eset)$condition == "A")]) / mean(exprs(eset)[1,unlist(pData(eset)$condition == "A")]))))
     + stopifnot(all.equal(cv[200,"C"] , sd(exprs(eset)[200,unlist(pData(eset)$condition == "C")]) / mean(exprs(eset)[200,unlist(pData(eset)$condition == "C")])))
     +
     + cvPaired <- getAllCV(esetPaired)
     + stopifnot(all(is.na(cvPaired[,1])))
     + stopifnot(all(!is.na(cvPaired[,2])))
     + stopifnot(cvPaired[3,"A"] == (sd(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6]) / mean(exprs(esetPaired)[3,1:2] / exprs(esetPaired)[3,5:6])))
     +
     + cat("--- testGetAllCV: PASS ALL TEST --- \n")
     + }
     >
     > testGlobalNormalize <- function(){
     +
     + cat("--- testGlobalNormalize: --- \n")
     +
     + globalNormFactors <- getGlobalNormFactors(eset,method="sum")
     + ### add normalization factors to ExpressionSet
     + pData(eset) <- cbind(pData(eset),globalNormFactors)
     + esetNorm <- globalNormalize(eset,globalNormFactors)
     +
     + stopifnot(all.equal(as.vector(unlist(apply(exprs(esetNorm),2,sum))),as.vector(rev(unlist(apply(exprs(esetNorm),2,sum))))))
     +
     + stopifnot(pData(esetNorm)$normFactor[1] == 1)
     + stopifnot(pData(esetNorm)$normFactor[2] != 1)
     +
     + cat("--- testGlobalNormalize: PASS ALL TEST --- \n")
     +
     + # Should generate error and stop
     + # fData(eset)$isNormAnchor <- rep(F,nrow(eset))
     + # esetNorm <- normalizeIntensities(eset)
     +
     + }
     >
     > testGetSignalPerCondition <- function(){
     +
     + cat("--- testGetSignalPerCondition: --- \n")
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"A"] <= getSignalPerCondition(eset,method="max")[,"A"]) == nrow(eset))
     + stopifnot(sum(getSignalPerCondition(eset,method="min")[,"C"] <= getSignalPerCondition(eset,method="median")[,"C"]) == nrow(eset))
     + stopifnot(getSignalPerCondition(eset,method="sd")[1,2] == sd(exprs(eset)[1,3:4]))
     + cat("--- testGetSignalPerCondition: PASS ALL TEST --- \n")
     + }
     >
     > testBaselineIntensity <- function(){
     +
     + cat("--- testBaselineIntensity: --- \n")
     +
     + allInt <- as.vector(unlist(exprs(eset)))
     + bl <- round(getBaselineIntensity(allInt,promille=5),2)
     + #hist(allInt)
     + #abline(v=bl,lwd=2)
     + stopifnot(all.equal(bl[[1]] , 997.82) )
     +
     +
     + set.seed(1234)
     + suppressWarnings(allInt2 <- log10(rnorm(1000,1,1)))
     + bl2 <- round(getBaselineIntensity(allInt2,promille=5),2)
     + stopifnot(all.equal(-1.95,bl2[[1]]))
     + #hist(allInt2)
     + #abline(v=bl2,lwd=2)
     +
     + cat("--- testBaselineIntensity: PASS ALL TEST --- \n")
     +
     + }
     >
     > testRollUp <- function(){
     +
     + cat(" --- testRollUp --- \n")
     +
     + rollUpEset1 <- rollUp(eset,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$proteinName ) ) == nrow(rollUpEset1))
     +
     + rollUpEset2 <- rollUp(eset ,featureDataColumnName= c("ptm"), method=c("sum"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset2))
     +
     + rollUpEset3 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("ptm"), method=c("mean"))
     + stopifnot( length( unique( fData(eset)$ptm ) ) == nrow(rollUpEset3))
     +
     + #print(exprs(rollUpEset2))
     +
     + stopifnot(all.equal(sum(exprs(rollUpEset2)),sum(exprs(rollUpEset1)))) ### test sum
     + stopifnot(sum(exprs(rollUpEset1)) != sum(exprs(rollUpEset3))) ### test mean
     +
     + rollUpEset4 <- rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))
     + stopifnot(sum(exprs(rollUpEset3)) != sum(exprs(rollUpEset4)) ) ### test top 3
     +
     + cat(" --- testRollUp: PASS ALL TEST --- \n")
     +
     + # progenesisFeatureCsvFile3 <- "/Users/ahrnee-adm/dev/R/workspace/SafeQuant/inst/testData/2014/peptides2.csv"
     + # d <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile3,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile3))
     + # system.time(e <- rollUp(d, method="sum", isProgressBar=T, featureDataColumnName= c("peptide")))
     + # system.time(e <- rollUpDT(d, method="sum", featureDataColumnName= c("peptide")))
     + #
     + esetTmp <- parseProgenesisPeptideMeasurementCsv(progenesisPeptideMeasurementCsvFile1,expDesign= getExpDesignProgenesisCsv(progenesisPeptideMeasurementCsvFile1))
     +
     + fData(esetTmp)
     +
     + rollUpEsetProteinAllAccessions <- rollUp(esetTmp,featureDataColumnName= c("proteinName"), method=c("sum"))
     + stopifnot(fData(rollUpEsetProteinAllAccessions)$allAccessionsTMP[68] == "sp|E9PAV3|NACAM_HUMAN;sp|Q9BZK3|NACP1_HUMAN")
     +
     + }
     >
     > testTopX <- function(){
     +
     + cat(" --- testTopX --- \n")
     +
     + entryData1 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,5),ncol=4)))
     + rownames(entryData1) <- paste("peptide",1:nrow(entryData1),sep="_")
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 5
     + stopifnot(all.equal(rep(10/3,3) , as.vector(unlist(getTopX(entryData1))) ))
     +
     + entryData2 <- data.frame(t(matrix(c(1,1,1,3,3,3,2,2,2,5,5,NA),ncol=4)))
     + rownames(entryData2) <- paste("peptide",1:nrow(entryData2),sep="_")
     +
     + # X1 X2 X3
     + # peptide_1 1 1 1
     + # peptide_2 3 3 3
     + # peptide_3 2 2 2
     + # peptide_4 5 5 NA
     + stopifnot(all.equal(c(4,4,3) , as.vector(unlist(getTopX(entryData2,topX=2)))))
     +
     + # 1 row
     + stopifnot(all.equal(rep(1,3),as.vector(unlist(getTopX(entryData1[1,])))))
     +
     + # 1 col
     + stopifnot(all.equal(getTopX(entryData1)[[1]],getTopX(entryData1[,1])))
     +
     + top1 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top1"))),1,sum)
     + top3 <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("top3"))),1,sum)
     + meanInt <- apply(exprs(rollUp(eset[!fData(eset)$isFiltered,] ,featureDataColumnName= c("proteinName"), method=c("mean"))),1,sum)
     +
     + stopifnot(sum(top1 >= top3 ) == length(top3))
     + stopifnot(sum(top1) > sum(top3))
     + stopifnot(sum(top1) > sum(meanInt))
     + stopifnot(all.equal(sum(top3),sum(meanInt)))
     +
     + cat(" --- testTopX: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetIBAQEset <- function(){
     +
     + cat(" --- testGetIBAQEset --- \n")
     +
     + # read protein fasta
     + proteinDB <- read.fasta(fastaFile,seqtype = "AA",as.string = TRUE, set.attributes = FALSE)
     +
     + iBaqEset <- getIBAQEset(eset,proteinDB=proteinDB)
     + stopifnot(round(exprs(iBaqEset))[1,1] == 125)
     + stopifnot(round(exprs(iBaqEset))[2,2] == 38)
     +
     + cat(" --- testGetIBAQEset: PASS ALL TEST --- \n")
     + }
     >
     >
     > testGetLoocvFoldError <- function(){
     +
     + cat(" --- testGetLoocvFoldError --- \n")
     + #plotCalibrationCurve(fit)
     + stopifnot( round(sum(getLoocvFoldError(absEstSimData))) == -8)
     + cat(" --- testGetLoocvFoldError: PASS ALL TEST --- \n")
     + }
     >
     > testSqNormalize <- function(){
     +
     + cat(" --- testSqNormalize --- \n")
     +
     + stopifnot(nrow(sqNormalize(eset, method = "global")) == 900)
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + stopifnot(nrow(sqNormalize(esetTmp, method = "rt")) == 496)
     +
     + cat(" --- testSqNormalize: PASS ALL TEST --- \n")
     + }
     >
     >
     > testRtNormalize <- function(){
     +
     +
     + cat(" --- testRTNormalize --- \n")
     + esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
     + rtNormFactors <- getRTNormFactors(esetTmp, minFeaturesPerBin=100)
     + stopifnot(nrow(rtNormalize(esetTmp,rtNormFactors)) == 97)
     +
     + # Stop if rtNormFactors doesn't cover all retention times.
     + #rtNormalize(esetTmp,rtNormFactors[1:2,])
     +
     + cat(" --- testRTNormalize: PASS ALL TEST --- \n")
     + }
     >
     > testRemoveOutliers <- function(){
     +
     + cat(" --- testRemoveOutliers --- \n")
     + set.seed(1234)
     + stopifnot(sum(is.na(removeOutliers(c(-10, rnorm(100), 10)))) == 2)
     + cat(" --- testRemoveOutliers: PASS ALL TEST --- \n")
     + }
     >
     > testPerFeatureNormalization <- function(){
     +
     + cat(" --- testPerFeatureNormalization: --- \n")
     +
     + normFactors <- exprs(eset)[1:10,1:3]
     + colnames(normFactors) <- c("A","B","C")
     + rownames(normFactors) <- fData(eset)[1:10,]$proteinName
     + normFactors[is.finite(normFactors)] <- 1
     + eNorm <- perFeatureNormalization(eset,normFactors)
     +
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,2] , (exprs(eset)[1,2]-1)))
     + stopifnot(all.equal(exprs(eNorm)[13,2] , (exprs(eset)[13,2])))
     +
     + normFactors[,2] <- 200
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,1] , (exprs(eset)[1,1]-1)))
     + stopifnot(all.equal(exprs(eNorm)[1,3] , (exprs(eset)[1,3]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,4] , (exprs(eset)[1,4]-200)))
     + stopifnot(all.equal(exprs(eNorm)[1,5] , (exprs(eset)[1,5]-1)))
     +
     + normFactors[,3] <- 0
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[1,5] , exprs(eset)[1,5]))
     + stopifnot(all.equal(exprs(eNorm)[2,6] , exprs(eset)[2,6]))
     +
     + normFactors[3,] <- 1000
     + eNorm <- perFeatureNormalization(eset,normFactors)
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + # re-order normFactors columns
     + eNorm <- perFeatureNormalization(eset,normFactors[,rev(colnames(normFactors))])
     + stopifnot(all.equal(exprs(eNorm)[3,] , (exprs(eset)[3,]-1000)))
     + stopifnot(all.equal(exprs(eNorm)[20:50,] , exprs(eset)[20:50,]))
     +
     + cat(" --- testPerFeatureNormalization: PASS ALL TEST --- \n")
     +
     + #coveredPeptideSel <- fData(eset)$proteinName %in% rownames(normFactors)
     + #exprs(eset)[coveredPeptideSel,] <- exprs(eset)[coveredPeptideSel, ] - normFactors[as.character(fData(eset)[coveredPeptideSel,]$proteinName),pData(eset)$condition]
     +
     + }
     >
     >
     > testStandardise <- function(){
     +
     + cat(" --- testStandardise: --- \n")
     +
     + d <- data.frame(rnorm(10000,5,20), rnorm(10000,10,10))
     + dStd <- standardise(d[,1])
     +
     + stopifnot(round(mean(dStd)) == 0 )
     + stopifnot(round(sd(dStd)) == 1 )
     +
     + dStd <- standardise(d)
     + stopifnot(round(apply(dStd,2,mean)[1]) == 0)
     + stopifnot(round(apply(dStd,2,sd)[1]) == 1)
     +
     + cat(" --- testStandardise: PASS ALL TEST --- \n")
     +
     + }
     >
     > testGetMaxIndex <-function(){
     +
     + cat(" --- testGetMaxIndex: --- \n")
     + d <- data.frame(s=c(NA,NA,NA,NA,1,1:4),lab=sort(rep(c("A","B","C"),3)))
     + DT <- data.table(d)
     + setkey(DT,lab)
     +
     +
     + stopifnot(all.equal(c(1,5,9) , DT[, .I[getMaxIndex(s)], by=lab ]$V1 ))
     + cat(" --- testGetMaxIndex: PASS ALL TEST --- \n")
     +
     + }
     >
     > testCreatePairedExpDesign <- function(){
     +
     + cat(" --- testCreatePairedExpDesign: --- \n")
     + stopifnot(all( pData(createPairedExpDesign(eset))$subject == as.factor(rep(1:2,3))))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:3]), silent = TRUE), "try-error")))
     + stopifnot((inherits(try(createPairedExpDesign(eset[,1:4]), silent = TRUE), "ExpressionSet")))
     + cat(" --- testCreatePairedExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     > ### TEST FUNCTIONS END
     >
     > #### TESTS
     > #testGetRatios()
     > #testGetAllEBayes()
     > #testGetSignalPerCondition()
     > #testGetRatios()
     >
     > if(T){
     + testCreateExpressionDataset()
     + testGetAllEBayes()
     + testGetRatios()
     + testGetAllCV()
     + testGlobalNormalize()
     + #testNormalise()
     + testRtNormalize()
     +
     + testBaselineIntensity()
     + testRollUp()
     + testTopX()
     +
     + testGetLoocvFoldError()
     +
     + testRemoveOutliers()
     + testPerFeatureNormalization()
     + testStandardise()
     + testGetMaxIndex()
     +
     + testGetIBAQEset()
     +
     + testCreatePairedExpDesign()
     +
     + }
     --- testCreateExpressionDataset: ---
     Error in testCreateExpressionDataset() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testCreateExpressionDataset -> stopifnot
     Execution halted
    Running the tests in ‘tests/testUserOptions.R’ failed.
    Complete output:
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     >
     > # TODO: Add comment
     > #
     > # Author: ahrnee-adm
     > ###############################################################################
     >
     > ### INIT
     > if(!grepl("SafeQuant\\.Rcheck",getwd())){
     + setwd(dirname(sys.frame(1)$ofile))
     + }
     > source("initTestSession.R")
    
     Attaching package: 'gplots'
    
     The following object is masked from 'package:stats':
    
     lowess
    
    
     Attaching package: 'seqinr'
    
     The following object is masked from 'package:limma':
    
     zscore
    
     Loading required package: survival
     Package epiR 1.0-14 is loaded
     Type help(epi.about) for summary information
     Type browseVignettes(package = 'epiR') to learn how to use epiR for applied epidemiological analyses
    
    
     corrplot 0.84 loaded
     Loading required package: BiocGenerics
     Loading required package: parallel
    
     Attaching package: 'BiocGenerics'
    
     The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
     The following object is masked from 'package:limma':
    
     plotMA
    
     The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
     The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
     Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
     > ### INIT END
     >
     >
     > ### TEST FUNCTIONS
     >
     > testExpDesignTagToExpDesign <- function(){
     +
     + cat("--- testExpDesignTagToExpDesign: --- \n")
     +
     + stopifnot(all.equal(pData(eset),expDesign))
     + stopifnot(all.equal(sampleNames(eset),colnames(m)))
     + stopifnot(all.equal(nrow(exprs(eset)),nrow(m)))
     +
     + expDesignString1 <- "1,2,3:4,5,6"
     +
     + # 6-plex default: 1,2,3:4,5,6
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 1 TRUE
     + #3 Condition 1 TRUE
     + #4 Condition 2 FALSE
     + #5 Condition 2 FALSE
     + #6 Condition 2 FALSE
     +
     +
     + expDesign <- data.frame(condition=paste("Condition",sort(rep(c(1,2),3))),isControl=sort(rep(c(T,F),3),decreasing=T) )
     +
     + expDesign1 <- expDesignTagToExpDesign(expDesignString1, expDesign)
     +
     + stopifnot(nrow(expDesign1) == 6 )
     + stopifnot(length(unique(expDesign1$condition)) == 2 )
     + stopifnot(sum(expDesign1$isControl) == 3 )
     +
     + expDesignString2 <- "1,4,7,10:2,5,8:3,6,9"
     +
     + # 10-plex default is "1,4,7,10:2,5,8:3,6,9"
     + #condition isControl
     + #1 Condition 1 TRUE
     + #2 Condition 2 FALSE
     + #3 Condition 3 FALSE
     + #4 Condition 1 TRUE
     + #5 Condition 2 FALSE
     + #6 Condition 3 FALSE
     + #7 Condition 1 TRUE
     + #8 Condition 2 FALSE
     + #9 Condition 3 FALSE
     + #10 Condition 1 TRUE
     +
     + expDesign <- data.frame(condition=paste("Condition",c(1,2,3,1,2,3,1,2,3,1)),isControl=c(T,F,F,T,F,F,T,F,F,T) )
     + expDesign2 <- expDesignTagToExpDesign(expDesignString2, expDesign)
     + stopifnot(nrow(expDesign2) == 10 )
     + stopifnot(length(unique(expDesign2$condition)) == 3 )
     + stopifnot(sum(expDesign2$isControl) == 4 )
     +
     + ### condition name assignment when mixing runs from different conditions
     + expDesign <- data.frame(condition=paste("foo",c(1,1,1,2,2,3,3)),isControl=c(F,F,F,T,T,F,F) )
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5:6",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1:4,6:5",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("1,2,3:4,5",expDesign)$condition)))
     + stopifnot(all(grepl("Condition" ,expDesignTagToExpDesign("1,2,4",expDesign)$condition)))
     + stopifnot(all(grepl("foo" ,expDesignTagToExpDesign("2",expDesign)$condition)))
     + stopifnot( length(unique(expDesignTagToExpDesign("1:2:3:4:5:6",expDesign)$condition)) == 6)
     +
     + cat("--- testExpDesignTagToExpDesign: PASS ALL TEST --- \n")
     +
     + }
     >
     >
     > ### TEST FUNCTIONS END
     >
     > ### TESTS
     > testExpDesignTagToExpDesign()
     --- testExpDesignTagToExpDesign: ---
     Error in testExpDesignTagToExpDesign() :
     pData(eset) and expDesign are not equal:
     Component "condition": 'current' is not a factor
     Calls: testExpDesignTagToExpDesign -> stopifnot
     Execution halted
Flavor: r-patched-solaris-x86