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> ### > attach(NULL, name = "CheckExEnv") > assign(".CheckExEnv", as.environment(2), pos = length(search())) # base > ## add some hooks to label plot pages for base and grid graphics > setHook("plot.new", ".newplot.hook") > setHook("persp", ".newplot.hook") > setHook("grid.newpage", ".gridplot.hook") > > assign("cleanEx", + function(env = .GlobalEnv) { + rm(list = ls(envir = env, all.names = TRUE), envir = env) + RNGkind("default", "default") + set.seed(1) + options(warn = 1) + delayedAssign("T", stop("T used instead of TRUE"), + assign.env = .CheckExEnv) + delayedAssign("F", stop("F used instead of FALSE"), + assign.env = .CheckExEnv) + sch <- search() + newitems <- sch[! sch %in% .oldSearch] + for(item in rev(newitems)) + eval(substitute(detach(item), list(item=item))) + missitems <- .oldSearch[! .oldSearch %in% sch] + if(length(missitems)) + warning("items ", paste(missitems, collapse=", "), + " have been removed from the search path") + }, + env = .CheckExEnv) > assign("..nameEx", "__{must remake R-ex/*.R}__", env = .CheckExEnv) # for now > assign("ptime", proc.time(), env = .CheckExEnv) > grDevices::postscript("LMGene-Examples.ps") > assign("par.postscript", graphics::par(no.readonly = TRUE), env = .CheckExEnv) > options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly")) > options(warn = 1) > library('LMGene') Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: multtest Loading required package: survival Loading required package: splines Loading required package: genefilter Loading required package: survival Loading required package: reposTools > > assign(".oldSearch", search(), env = .CheckExEnv) > assign(".oldNS", loadedNamespaces(), env = .CheckExEnv) > cleanEx(); ..nameEx <- "LMGene" > > ### * LMGene > > flush(stderr()); flush(stdout()) > > ### Name: LMGene > ### Title: LMGene main function > ### Aliases: LMGene > ### Keywords: models > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd) > data(vlist) > LoggedSmpd0<-neweS(lnorm(log(Smpd)),vlist) > > siggeneslist<-LMGene(LoggedSmpd0, 0.01) > siggeneslist$x3 [1] "690" > > > > > cleanEx(); ..nameEx <- "Smpd" > > ### * Smpd > > flush(stderr()); flush(stdout()) > > ### Name: Smpd > ### Title: Sample array data for LMGene package > ### Aliases: Smpd > ### Keywords: datasets > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd) > data(vlist) > > Smpdt<-neweS(Smpd,vlist) > > data(Smpd0) > identical(Smpd0, Smpdt) [1] FALSE > > > > cleanEx(); ..nameEx <- "Smpd0" > > ### * Smpd0 > > flush(stderr()); flush(stdout()) > > ### Name: Smpd0 > ### Title: Sample array data for LMGene > ### Aliases: Smpd0 > ### Keywords: datasets > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd) > data(vlist) > > Smpdt<-neweS(Smpd,vlist) > > data(Smpd0) > identical(Smpd0, Smpdt) [1] FALSE > > > > cleanEx(); ..nameEx <- "arrplot1" > > ### * arrplot1 > > flush(stderr()); flush(stdout()) > > ### Name: arrplot1 > ### Title: Function to calculate relative mean squares > ### Aliases: arrplot1 > ### Keywords: dplot > > ### ** Examples > > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd0) > > # > RMS<-arrplot1(Smpd0) > RMS[,1:5] resmat tmp4 tmp4 tmp4 tmp4 dye 0.1011772 0.270523261 0.019697866 0.097832188 0.499628068 slide 0.5708201 0.664532435 0.917237661 0.872747476 0.467161217 treat 0.2224454 0.003744267 0.001279869 0.002367297 0.008114993 Error 0.1055573 0.061200037 0.061784604 0.027053038 0.025095723 > > > > cleanEx(); ..nameEx <- "arrplotd" > > ### * arrplotd > > flush(stderr()); flush(stdout()) > > ### Name: arrplotd > ### Title: Function for plotting a smoothed histogram > ### Aliases: arrplotd > ### Keywords: hplot > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd0) > > # > arrplotd(Smpd0) > > > > > cleanEx(); ..nameEx <- "arrplote" > > ### * arrplote > > flush(stderr()); flush(stdout()) > > ### Name: arrplote > ### Title: Function for plotting a cumulative frequency distribution > ### Aliases: arrplote > ### Keywords: hplot > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd0) > > # > arrplote(Smpd0) > > > > cleanEx(); ..nameEx <- "beams" > > ### * beams > > flush(stderr()); flush(stdout()) > > ### Name: beams > ### Title: Beam search rountine for finding the optimal parameters > ### Aliases: beams > ### Keywords: optimize > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd0) > > # > mat1 <- as.matrix(Smpd0@exprs) > lamstart <- log(median(abs(mat1))^2) > alphastart <- quantile(abs(as.vector(mat1)), 0.1) > startvar <- c(lamstart, alphastart) > > beams(Smpd0, startvar) [1] 625.15409 59.33514 > > > > cleanEx(); ..nameEx <- "dplot" > > ### * dplot > > flush(stderr()); flush(stdout()) > > ### Name: dplot > ### Title: Plotting smoothed histogram > ### Aliases: dplot > ### Keywords: hplot > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd0) > > # > RMS<-arrplot1(Smpd0) > dplot(RMS, "Example") > > > > > cleanEx(); ..nameEx <- "dplote" > > ### * dplote > > flush(stderr()); flush(stdout()) > > ### Name: dplote > ### Title: Plotting cumulative frequency distribution > ### Aliases: dplote > ### Keywords: hplot > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd0) > > # > RMS<-arrplot1(Smpd0) > dplote(RMS, "Example") > > > > > cleanEx(); ..nameEx <- "genediff" > > ### * genediff > > flush(stderr()); flush(stdout()) > > ### Name: genediff > ### Title: Raw p-value calculation function > ### Aliases: genediff > ### Keywords: models > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd) > data(vlist) > LoggedSmpd0<-neweS(lnorm(log(Smpd)),vlist) > > pvlist<-genediff(LoggedSmpd0) > pvlist$Posterior[1:5,] x1 x2 x3 [1,] 0.0001476389 0.0876451961 0.01710396 [2,] 0.0036824889 0.4460457229 0.92331289 [3,] 0.0015554714 0.0001157710 0.75944849 [4,] 0.2547516155 0.1831986170 0.83650471 [5,] 0.0017216158 0.0010111314 0.54689814 > > > > > cleanEx(); ..nameEx <- "glog" > > ### * glog > > flush(stderr()); flush(stdout()) > > ### Name: glog > ### Title: Generalized log transformation function > ### Aliases: glog > ### Keywords: math > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd) > Smpd[1:5,1:4] X1 X2 X3 X4 780 355 311 175 224 297 95 102 89 119 939 123 104 104 85 611 99 127 84 111 928 164 295 135 275 > > GloggedSmpd<-glog(Smpd-50,500) > GloggedSmpd[1:5,1:4] X1 X2 X3 X4 780 6.414800 6.259498 5.529367 5.856306 297 4.556498 4.687707 4.430287 4.952531 939 5.006278 4.722478 4.722478 4.337724 611 4.633378 5.057398 4.313399 4.836038 928 5.438828 6.196481 5.152667 6.111708 > > > > > cleanEx(); ..nameEx <- "jggrad2" > > ### * jggrad2 > > flush(stderr()); flush(stdout()) > > ### Name: jggrad2 > ### Title: Generating Jacobian-corrected data > ### Aliases: jggrad2 > ### Keywords: math > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd) > dim(Smpd) [1] 500 16 > > JCSmpd<-jggrad2(Smpd, 500, 50) > dim(JCSmpd) [1] 500 48 > > > > > cleanEx(); ..nameEx <- "jglog" > > ### * jglog > > flush(stderr()); flush(stdout()) > > ### Name: jglog > ### Title: Glog > ### Aliases: jglog > ### Keywords: math > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd) > Smpd[1:5,1:4] X1 X2 X3 X4 780 355 311 175 224 297 95 102 89 119 939 123 104 104 85 611 99 127 84 111 928 164 295 135 275 > > GloggedSmpd<-glog(Smpd-50,500) > GloggedSmpd[1:5,1:4] X1 X2 X3 X4 780 6.414800 6.259498 5.529367 5.856306 297 4.556498 4.687707 4.430287 4.952531 939 5.006278 4.722478 4.722478 4.337724 611 4.633378 5.057398 4.313399 4.836038 928 5.438828 6.196481 5.152667 6.111708 > > > > > cleanEx(); ..nameEx <- "lnorm" > > ### * lnorm > > flush(stderr()); flush(stdout()) > > ### Name: lnorm > ### Title: Lowess normalization function > ### Aliases: lnorm > ### Keywords: math > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd) > LoggedSmpd<-lnorm(log(Smpd)) > > > > > cleanEx(); ..nameEx <- "mlm2lm" > > ### * mlm2lm > > flush(stderr()); flush(stdout()) > > ### Name: mlm2lm > ### Title: Linear Model converting function > ### Aliases: mlm2lm > ### Keywords: models > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd0) > > # model information > for(i in 1:length(Smpd0@phenoData@varLabels)){ + assign(paste('x', i, sep=''),as.factor(Smpd0@phenoData@pData[,i])) + } > > fchar='' > for(i in 1:length(Smpd0@phenoData@varLabels)){ + fchar=paste(fchar, paste('x', i, sep=''), ifelse(i fchar2 <- paste("y ~",fchar) > # > # run regression and anovas > y <- t(as.matrix(Smpd0@exprs)) > formobj <- as.formula(fchar2) > tmp <- lm(formobj) > class(tmp) [1] "mlm" "lm" > > tmp2 <- mlm2lm(tmp,i) > class(tmp2) [1] "lm" > > > > > cleanEx(); ..nameEx <- "msa" > > ### * msa > > flush(stderr()); flush(stdout()) > > ### Name: msa > ### Title: Relative mean square calculation function > ### Aliases: msa > ### Keywords: math > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > #data > data(Smpd0) > > # model information > for(i in 1:length(Smpd0@phenoData@varLabels)){ + assign(paste('x', i, sep=''),as.factor(Smpd0@phenoData@pData[,i])) + } > > fchar='' > for(i in 1:length(Smpd0@phenoData@varLabels)){ + fchar=paste(fchar, paste('x', i, sep=''), ifelse(i fchar2 <- paste("y ~",fchar) > # > # run regression and anovas > y <- t(as.matrix(Smpd0@exprs)) > formobj <- as.formula(fchar2) > tmp <- lm(formobj) > tmp2 <- mlm2lm(tmp,i) > tmp3 <- anova(tmp2)$Mean > tmp4 <- msa(tmp3) > rbind(tmp3, tmp4) [,1] [,2] [,3] [,4] tmp3 162.56250000 7569.7767857 10.562500000 509.8958333 tmp4 0.01969787 0.9172377 0.001279869 0.0617846 > > > > > cleanEx(); ..nameEx <- "msecalc" > > ### * msecalc > > flush(stderr()); flush(stdout()) > > ### Name: msecalc > ### Title: MSE calculation function > ### Aliases: msecalc > ### Keywords: math > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd0) > > msecalc(Smpd0,500,50, FALSE) [1] 2.828441e+03 7.459658e-02 5.919955e-01 > > > > > cleanEx(); ..nameEx <- "neweS" > > ### * neweS > > flush(stderr()); flush(stdout()) > > ### Name: neweS > ### Title: Coercing to exprSet function > ### Aliases: neweS > ### Keywords: manip > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd) > data(vlist) > > Smpdt<-neweS(Smpd,vlist) > > data(Smpd0) > identical(Smpd0, Smpdt) [1] FALSE > > > > > cleanEx(); ..nameEx <- "norm" > > ### * norm > > flush(stderr()); flush(stdout()) > > ### Name: norm > ### Title: Additive normalization function > ### Aliases: norm > ### Keywords: math > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd) > LoggedSmpd<-norm(log(Smpd)) > > > > > cleanEx(); ..nameEx <- "pvadjust" > > ### * pvadjust > > flush(stderr()); flush(stdout()) > > ### Name: pvadjust > ### Title: P-value adjusting function > ### Aliases: pvadjust > ### Keywords: models > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd) > data(vlist) > LoggedSmpd0<-neweS(lnorm(log(Smpd)),vlist) > > pvlist<-genediff(LoggedSmpd0) > pvlist$Posterior[1:5,] x1 x2 x3 [1,] 0.0001476389 0.0876451961 0.01710396 [2,] 0.0036824889 0.4460457229 0.92331289 [3,] 0.0015554714 0.0001157710 0.75944849 [4,] 0.2547516155 0.1831986170 0.83650471 [5,] 0.0017216158 0.0010111314 0.54689814 > > apvlist<-pvadjust(pvlist) > names(apvlist) [1] "Gene.Specific" "Posterior" "Gene.Specific.FDR" [4] "Posterior.FDR" > apvlist$Posterior.FDR[1:5,] x1 x2 x3 [1,] 0.0007896538 0.173211850 0.2298285 [2,] 0.0107049097 0.537810457 0.9906463 [3,] 0.0052234923 0.001371723 0.9239033 [4,] 0.3538216882 0.291717543 0.9549596 [5,] 0.0056632099 0.006652180 0.8138365 > > > > > cleanEx(); ..nameEx <- "rgplot" > > ### * rgplot > > flush(stderr()); flush(stdout()) > > ### Name: rgplot > ### Title: Plotting density function > ### Aliases: rgplot > ### Keywords: hplot > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd0) > > # > rgplot(Smpd0) > > > > > cleanEx(); ..nameEx <- "rowaov" > > ### * rowaov > > flush(stderr()); flush(stdout()) > > ### Name: rowaov > ### Title: Gene by gene anova functioin > ### Aliases: rowaov > ### Keywords: models > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd) > data(vlist) > LoggedSmpd0<-neweS(lnorm(log(Smpd)),vlist) > > resmat <- rowaov(LoggedSmpd0) > resmat[,1:3] resmat tmp4 tmp4 [1,] 0.364946133 0.1853291842 0.465846986 [2,] 0.027883185 0.0144990311 0.375625368 [3,] 0.089100076 0.0001325032 0.002615388 [4,] 0.007303965 0.0116175203 0.034872886 [5,] 1.000000000 1.0000000000 1.000000000 [6,] 7.000000000 7.0000000000 7.000000000 [7,] 1.000000000 1.0000000000 1.000000000 [8,] 6.000000000 6.0000000000 6.000000000 > > > > cleanEx(); ..nameEx <- "rowlist" > > ### * rowlist > > flush(stderr()); flush(stdout()) > > ### Name: rowlist > ### Title: Gene name listing function > ### Aliases: rowlist > ### Keywords: manip > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd) > data(vlist) > LoggedSmpd0<-neweS(lnorm(log(Smpd)),vlist) > > pvlist<-genediff(LoggedSmpd0) > apvlist<-pvadjust(pvlist) > > genelist<-rowlist(LoggedSmpd0@exprs,3,apvlist,0.01) > genelist [1] "690" > > > > > cleanEx(); ..nameEx <- "tranest" > > ### * tranest > > flush(stderr()); flush(stdout()) > > ### Name: tranest > ### Title: Glog transformation parameter estimation function > ### Aliases: tranest > ### Keywords: math > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd0) > > tranpar <- tranest(Smpd0, 100, FALSE, 500, 50, 1e-3, FALSE) > tranpar $lambda [1] 1224.538 $alpha [1] 70.50191 > tranpar <- tranest(Smpd0, -1, FALSE, 500, 50, 1e-3, FALSE) > tranpar $lambda [1] 625.1541 $alpha [1] 59.33514 > > > > > cleanEx(); ..nameEx <- "tranest2" > > ### * tranest2 > > flush(stderr()); flush(stdout()) > > ### Name: tranest2 > ### Title: Glog transformation parameter estimation function 2 > ### Aliases: tranest2 > ### Keywords: math > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(Smpd0) > > tranpar <- tranest2(Smpd0, FALSE, 500, 50, 1e-3, FALSE) > tranpar [1] 625.15409 59.33514 > > > > > cleanEx(); ..nameEx <- "vlist" > > ### * vlist > > flush(stderr()); flush(stdout()) > > ### Name: vlist > ### Title: Sample experimental data for LMGene package > ### Aliases: vlist > ### Keywords: datasets > > ### ** Examples > > #library > library(Biobase) > library(LMGene) > > #data > data(vlist) > > vlist $dye [1] R G R G R G R G R G R G R G R G Levels: R G $slide [1] 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 Levels: 1 2 3 4 5 6 7 8 $treat [1] P S S P P S S P P S S P P S S P Levels: P S > > > > > ### *