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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("mscalib-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('mscalib') Loading required package: modreg Warning: package 'modreg' has been merged into 'stats' Attaching package: 'mscalib' The following object(s) are masked from package:base : mget > > assign(".oldSearch", search(), env = .CheckExEnv) > assign(".oldNS", loadedNamespaces(), env = .CheckExEnv) > cleanEx(); ..nameEx <- "..caliblist" > > ### * ..caliblist > > flush(stderr()); flush(stdout()) > > ### Name: [.caliblist > ### Title: Extract Parts of a Caliblist. > ### Aliases: [.caliblist > ### Keywords: misc > > ### ** Examples > > data(mvl) > data(cal) > print(cal) [1] info : (calib) [1] coor : ; mass C2 1 720.4000 1 2 842.5099 1 3 863.4100 1 4 1045.5642 1 5 1126.5478 1 6 1131.5500 1 7 1232.5400 1 8 1296.6853 1 9 1352.7000 1 10 1638.7800 1 11 1672.9175 1 12 2069.9300 1 13 2085.0400 1 14 2211.1046 1 15 2225.1203 1 16 2239.1359 1 17 2283.1807 1 18 2297.1964 1 19 2313.1913 1 20 2465.1980 1 21 2807.3290 1 22 2839.3048 1 23 3147.4715 1 24 3346.7120 1 25 3846.1200 1 > res<-getintcalib(mvl,cal,error=300) > res<-res[1:10] > class(res) [1] "calibintlist" "caliblist" "mlist" "list" "myobj" > plot(res) > > > > cleanEx(); ..nameEx <- "..massvector" > > ### * ..massvector > > flush(stderr()); flush(stdout()) > > ### Name: [.massvector > ### Title: Extract Parts of an Massvector > ### Aliases: [.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > ls() [1] "mv1" > mv1[1:10,] # returns a massvector of length 10 [1] info : (0_A1_1SRef) [1] coor : A=1 ; 1=1 mass area 1 842.4257 650.66 2 987.3931 180.30 3 1098.4314 3543.85 4 1112.4456 251.17 5 1129.4501 345.22 6 1147.4617 2261.36 7 1207.5648 1948.22 8 1257.5929 204.77 9 1296.6086 1528.91 10 1466.5645 257.75 > mv1[1:10,1] # the first ten masses are returned. 1 2 3 4 5 6 7 8 842.4257 987.3931 1098.4314 1112.4456 1129.4501 1147.4617 1207.5648 1257.5929 9 10 1296.6086 1466.5645 > mv1[,1] # the masses are returned. 1 2 3 4 5 6 7 8 842.4257 987.3931 1098.4314 1112.4456 1129.4501 1147.4617 1207.5648 1257.5929 9 10 11 12 13 14 15 16 1296.6086 1466.5645 1554.6257 1672.7671 1686.7343 1694.6771 1712.7915 1734.7188 17 18 19 20 21 22 23 24 1746.7566 1750.6805 1754.6996 1766.7008 1793.7116 1807.6837 1810.7358 1973.8298 25 26 27 28 29 30 31 32 2002.8374 2090.8222 2104.8344 2128.7796 2189.8599 2210.8834 2224.9057 2232.9109 33 34 35 36 37 38 39 40 2238.9288 2245.9799 2248.8393 2298.9676 2312.9932 2465.0143 2505.0601 2703.1986 41 42 43 44 45 46 47 48 2811.1438 2914.3276 3000.3723 3014.3788 3057.3808 3120.2176 3331.4928 3346.5022 49 3354.5540 > mv1[,2] # the peak area are returned. 1 2 3 4 5 6 7 8 650.66 180.30 3543.85 251.17 345.22 2261.36 1948.22 204.77 9 10 11 12 13 14 15 16 1528.91 257.75 600.61 5067.09 863.64 4959.24 619.39 665.85 17 18 19 20 21 22 23 24 574.26 7579.83 2695.35 402.83 1784.45 604.98 4088.75 1174.58 25 26 27 28 29 30 31 32 504.87 15183.35 1877.67 467.04 594.90 4582.26 1765.44 931.45 33 34 35 36 37 38 39 40 491.35 1913.02 727.08 2394.62 401.28 2196.50 360.43 1013.07 41 42 43 44 45 46 47 48 778.49 458.57 8538.46 1666.68 395.89 273.91 538.24 2513.62 49 415.73 > > > > cleanEx(); ..nameEx <- "..massvectorlist" > > ### * ..massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: [.massvectorlist > ### Title: Extract Parts of an Massvectorlist. > ### Aliases: [.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > mvl<-mvl[1:10] # returns a massvectorlist of length 10 > mvl [1] Experiment : (020529r_dt_Pirellula) [1] Project : () [1] Nr (mv) : (10) > class(mvl) [1] "massvectorlist" "mlist" "list" "myobj" > > > > cleanEx(); ..nameEx <- ".Assing.massvectorlist" > > ### * .Assing.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: [Assing.massvectorlist > ### Title: Replace Parts of Massvectorlist > ### Aliases: [Assing.massvectorlist [<-.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > mvl2<-mvl > mvl2[11:20]<-mvl[1:10] > compare(mvl[[11]],mvl[[1]]) > > > > cleanEx(); ..nameEx <- "..Assing.caliblist" > > ### * ..Assing.caliblist > > flush(stderr()); flush(stdout()) > > ### Name: [[Assing.caliblist > ### Title: Replace calibstat object in the caliblist. > ### Aliases: [[Assing.caliblist [[<-.caliblist > ### Keywords: misc > > ### ** Examples > > data(mvl) > data(cal) > res<-getintcalib(mvl,cal,error=300) > res[[1]]<-res[[10]] > > > > cleanEx(); ..nameEx <- "..Assing.massvectorlist" > > ### * ..Assing.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: [[Assing.massvectorlist > ### Title: Replace Parts of an Object > ### Aliases: [[Assing.massvectorlist [[<-.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > data(mv1) > mvl[[10]]<-mv1 > > > > cleanEx(); ..nameEx <- "applycalib.calibintlist" > > ### * applycalib.calibintlist > > flush(stderr()); flush(stdout()) > > ### Name: applycalib.calibintlist > ### Title: Internal Calibration > ### Aliases: applycalib.calibintlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > data(cal) > res<-getintcalib(mvl,cal,error=300) > mvl2<-applycalib(res,mvl) 10 20 30 40 50 60 70 80 90 100 > > > > cleanEx(); ..nameEx <- "applycalib.calibintstat" > > ### * applycalib.calibintstat > > flush(stderr()); flush(stdout()) > > ### Name: applycalib.calibintstat > ### Title: Internal Calibration > ### Aliases: applycalib.calibintstat > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(cal) > res<-getintcalib(mv1,cal,error=300) > mv2<- applycalib(res,mv1) > plot(mv1[,1],mv2[,1]-mv1[,1]) > > > > cleanEx(); ..nameEx <- "applycalib.calibrelist" > > ### * applycalib.calibrelist > > flush(stderr()); flush(stdout()) > > ### Name: applycalib.calibrelist > ### Title: Precalibration > ### Aliases: applycalib.calibrelist > ### Keywords: misc > > ### ** Examples > > data(mvl) > mvl<-mvl[1:100] > res<-getrecalib(mvl) > plot(res) > image(res,what="PQM") > mvlr<-applycalib(res,mvl) 10 20 30 40 50 60 70 80 90 100 > > > > cleanEx(); ..nameEx <- "applycalib.calibrestat" > > ### * applycalib.calibrestat > > flush(stderr()); flush(stdout()) > > ### Name: applycalib.calibrestat > ### Title: Precalibration > ### Aliases: applycalib.calibrestat > ### Keywords: misc > > ### ** Examples > > data(mv1) > res <- getrecalib(mv1) > plot(res) Warning in plot.calibstat(res) : Not implemented!! > mv2<-applycalib(res,mv1) > plot(mv1[,1],mv2[,1]-mv1[,1]) > > > > cleanEx(); ..nameEx <- "applycalib.calibspline" > > ### * applycalib.calibspline > > flush(stderr()); flush(stdout()) > > ### Name: applycalib.calibspline > ### Title: External Calbiration > ### Aliases: applycalib.calibspline > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(ppg) > res<- getextcalib(ppg,getPPGmasses(),error=150) Loading required package: modreg Warning: package 'modreg' has been merged into 'stats' > plot(res) > mv2<-applycalib(res,mv1) > compare(mv1,mv2,error=300) > rm(mv1,mv2) > data(mvl) > mvl<-mvl[1:100] > res<-applycalib(res,mvl) > > > > cleanEx(); ..nameEx <- "applyextcalib.massvector" > > ### * applyextcalib.massvector > > flush(stderr()); flush(stdout()) > > ### Name: applyextcalib.massvector > ### Title: External Calbiration > ### Aliases: applyextcalib.massvector > ### Keywords: misc > > ### ** Examples > > data(ppg) > data(mv1) > res<-getextcalib(ppg[[1]],getPPGmasses(),error=200) Loading required package: modreg Warning: package 'modreg' has been merged into 'stats' > mv2<-applyextcalib(mv1,res) > compare(mv1,mv2) > > > > cleanEx(); ..nameEx <- "applyextcalib.massvectorlist" > > ### * applyextcalib.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: applyextcalib.massvectorlist > ### Title: External Calbiration > ### Aliases: applyextcalib.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(ppg) > data(mvl) > res <- getextcalib(ppg,getPPGmasses(),error=150) Loading required package: modreg Warning: package 'modreg' has been merged into 'stats' > mvl2 <- applyextcalib(mvl,res) > > > > cleanEx(); ..nameEx <- "applyintcalib.massvector" > > ### * applyintcalib.massvector > > flush(stderr()); flush(stdout()) > > ### Name: applyintcalib.massvector > ### Title: Internal Calibration > ### Aliases: applyintcalib.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(cal) > res<-getintcalib(mv1,cal,error=300) > mv2<- applyintcalib(mv1,res) > plot(mv1[,1],mv2[,1]-mv1[,1]) > > > > cleanEx(); ..nameEx <- "applyintcalib.massvectorlist" > > ### * applyintcalib.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: applyintcalib.massvectorlist > ### Title: Internal Calibration > ### Aliases: applyintcalib.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > mvl<-mvl[1:100] > data(cal) > res <- getintcalib(mvl,cal,error=300,ppm=FALSE) > mvl2<-applyintcalib(mvl,res) > > > > cleanEx(); ..nameEx <- "applyrecalib.massvector" > > ### * applyrecalib.massvector > > flush(stderr()); flush(stdout()) > > ### Name: applyrecalib.massvector > ### Title: Precalibration > ### Aliases: applyrecalib.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > res <- getrecalib(mv1) > plot(res) Warning in plot.calibstat(res) : Not implemented!! > mv2<-applyrecalib(mv1,res) > compare(mv1,mv2) > > > > cleanEx(); ..nameEx <- "applyrecalib.massvectorlist" > > ### * applyrecalib.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: applyrecalib.massvectorlist > ### Title: Recalibration > ### Aliases: applyrecalib.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > res<-getrecalib(mvl) > summary(res) $info [1] "020529r_dt_Pirellula" $summary lengthmv Coef.Intercept Coef.Slope PQM Min. : 8.00 Min. :-0.25008 Min. :-114.93 Min. : 7.704 1st Qu.:25.00 1st Qu.:-0.10422 1st Qu.: 28.74 1st Qu.:10.270 Median :33.50 Median :-0.07850 Median : 84.97 Median :10.666 Mean :37.03 Mean :-0.05974 Mean : 122.92 Mean :10.536 3rd Qu.:49.25 3rd Qu.:-0.02094 3rd Qu.: 181.19 3rd Qu.:11.035 Max. :81.00 Max. : 0.22554 Max. : 560.04 Max. :11.990 Xcoor Ycoor Min. :1.00 Min. : 1.00 1st Qu.:2.00 1st Qu.: 6.00 Median :3.00 Median :12.00 Mean :2.84 Mean :12.06 3rd Qu.:4.00 3rd Qu.:18.00 Max. :5.00 Max. :24.00 > mvl2<-applyrecalib(mvl,res) > > > > cleanEx(); ..nameEx <- "as.data.frame.mlist" > > ### * as.data.frame.mlist > > flush(stderr()); flush(stdout()) > > ### Name: as.data.frame.mlist > ### Title: Data Frames > ### Aliases: as.data.frame.mlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > tmp <- as.data.frame(mvl) > names(mvl) [1] "0_A1_1SRef" "0_A10_1SRef" "0_A11_1SRef" "0_A12_1SRef" "0_A13_1SRef" [6] "0_A14_1SRef" "0_A15_1SRef" "0_A16_1SRef" "0_A17_1SRef" "0_A18_1SRef" [11] "0_A19_1SRef" "0_A2_1SRef" "0_A20_1SRef" "0_A21_1SRef" "0_A22_1SRef" [16] "0_A23_1SRef" "0_A24_1SRef" "0_A3_1SRef" "0_A4_1SRef" "0_A5_1SRef" [21] "0_A6_1SRef" "0_A7_1SRef" "0_A8_1SRef" "0_A9_1SRef" "0_B1_1SRef" [26] "0_B10_1SRef" "0_B11_1SRef" "0_B12_1SRef" "0_B13_1SRef" "0_B15_1SRef" [31] "0_B17_1SRef" "0_B19_1SRef" "0_B2_1SRef" "0_B21_1SRef" "0_B23_1SRef" [36] "0_B3_1SRef" "0_B4_1SRef" "0_B5_1SRef" "0_B6_1SRef" "0_B7_1SRef" [41] "0_B8_1SRef" "0_B9_1SRef" "0_C1_1SRef" "0_C10_1SRef" "0_C11_1SRef" [46] "0_C12_1SRef" "0_C13_1SRef" "0_C14_1SRef" "0_C15_1SRef" "0_C16_1SRef" [51] "0_C17_1SRef" "0_C18_1SRef" "0_C19_1SRef" "0_C2_1SRef" "0_C20_1SRef" [56] "0_C21_1SRef" "0_C22_1SRef" "0_C23_1SRef" "0_C24_1SRef" "0_C3_1SRef" [61] "0_C4_1SRef" "0_C5_1SRef" "0_C6_1SRef" "0_C7_1SRef" "0_C8_1SRef" [66] "0_C9_1SRef" "0_D1_1SRef" "0_D10_1SRef" "0_D11_1SRef" "0_D12_1SRef" [71] "0_D13_1SRef" "0_D15_1SRef" "0_D17_1SRef" "0_D19_1SRef" "0_D2_1SRef" [76] "0_D21_1SRef" "0_D23_1SRef" "0_D3_1SRef" "0_D4_1SRef" "0_D5_1SRef" [81] "0_D6_1SRef" "0_D7_1SRef" "0_D8_1SRef" "0_D9_1SRef" "0_E1_1SRef" [86] "0_E10_1SRef" "0_E11_1SRef" "0_E12_1SRef" "0_E13_1SRef" "0_E14_1SRef" [91] "0_E15_1SRef" "0_E16_1SRef" "0_E17_1SRef" "0_E18_1SRef" "0_E19_1SRef" [96] "0_E2_1SRef" "0_E20_1SRef" "0_E21_1SRef" "0_E22_1SRef" "0_E23_1SRef" > plot(tmp$lengthmv,tmp$mass.Min.) > data(mvl) > mvl<-mvl[1:100] > data(cal) > test<-getintcalib(mvl,cal,error=500) > tmp<-as.data.frame(test) > names(tmp) [1] "info" "lengthmv" "Coef.Intercept" [4] "Coef.Slope" "nrmatch" "Xcoor" [7] "Ycoor" "R.Squared" "Adjusted.R.squared" [10] "p.value" > > > > cleanEx(); ..nameEx <- "as.list.massvectorlist" > > ### * as.list.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: as.list.massvectorlist > ### Title: List > ### Aliases: as.list.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > res<-as.list(mvl) > class(res) [1] "list" > > > > cleanEx(); ..nameEx <- "as.matrix.massvector" > > ### * as.matrix.massvector > > flush(stderr()); flush(stdout()) > > ### Name: as.matrix.massvector > ### Title: Matrices > ### Aliases: as.matrix.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > res<-as.matrix(mv1) > class(res) [1] "matrix" > > > > cleanEx(); ..nameEx <- "as.matrix.mlist" > > ### * as.matrix.mlist > > flush(stderr()); flush(stdout()) > > ### Name: as.matrix.mlist > ### Title: Matrices > ### Aliases: as.matrix.mlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > mvl<-mvl[1:100] > data(cal) > test<-getintcalib(mvl,cal,error=500) > tmp<-as.matrix(test) > colnames(tmp) [1] "lengthmv" "Coef.Intercept" "Coef.Slope" [4] "nrmatch" "Xcoor" "Ycoor" [7] "R.Squared" "Adjusted.R.squared" "p.value" > dim(tmp) [1] 100 9 > data(mvl) > tmp<-as.matrix(mvl) > print(colnames(mvl)) NULL > plot(tmp[,"lengthmv"],tmp[,"mass.Min."]) > > > > cleanEx(); ..nameEx <- "as.vector.calibintstat" > > ### * as.vector.calibintstat > > flush(stderr()); flush(stdout()) > > ### Name: as.vector.calibintstat > ### Title: Coerces to vectors > ### Aliases: as.vector.calibintstat > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(cal) > res<-getintcalib(mv1,cal,error=500,ppm=TRUE) > as.vector(res) lengthmv Coef.Intercept Coef.Slope nrmatch 49.00000000 98.17173773 -65.96179571 9.00000000 Xcoor Ycoor R.Squared Adjusted.R.squared 1.00000000 1.00000000 0.09409140 -0.03532411 p.value 0.42205418 > > > > cleanEx(); ..nameEx <- "as.vector.calibrestat" > > ### * as.vector.calibrestat > > flush(stderr()); flush(stdout()) > > ### Name: as.vector.calibrestat > ### Title: Coerces to vector > ### Aliases: as.vector.calibrestat > ### Keywords: misc > > ### ** Examples > > data(mv1) > res<-getrecalib(mv1) > as.vector(res) lengthmv Coef.Intercept Coef.Slope PQM Xcoor 49.00000000 0.05744198 44.97975911 11.22154876 1.00000000 Ycoor 1.00000000 > > > > cleanEx(); ..nameEx <- "as.vector.massvector" > > ### * as.vector.massvector > > flush(stderr()); flush(stdout()) > > ### Name: as.vector.massvector > ### Title: Vector > ### Aliases: as.vector.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > as.vector(mv1) lengthmv mass.Min. mass.1st Qu. mass.Median mass.Mean mass.3rd Qu. 49.0 842.4 842.4 842.4 842.4 842.4 mass.Max. area.Min. area.1st Qu. area.Median area.Mean area.3rd Qu. 842.4 650.7 650.7 650.7 650.7 650.7 area.Max. 650.7 > > > > cleanEx(); ..nameEx <- "c.massvector" > > ### * c.massvector > > flush(stderr()); flush(stdout()) > > ### Name: c.massvector > ### Title: Combine Massvectors into one Massvector. > ### Aliases: c.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(mv2) > par(mfrow=c(2,1)) > plot(mv1) > plot(mv2,add=TRUE) > plot(c(mv1,mv2)) > > > > graphics::par(get("par.postscript", env = .CheckExEnv)) > cleanEx(); ..nameEx <- "c.massvectorlist" > > ### * c.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: c.massvectorlist > ### Title: Combine > ### Aliases: c.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > mvl2<-c(mvl[1:100],mvl[1:50]) > mvl2 [1] Experiment : (020529r_dt_Pirellula) [1] Project : () [1] Nr (mv) : (150) > > > > cleanEx(); ..nameEx <- "calibexternal.massvector" > > ### * calibexternal.massvector > > flush(stderr()); flush(stdout()) > > ### Name: calibexternal.massvector > ### Title: External Calbiration > ### Aliases: calibexternal.massvector > ### Keywords: misc > > ### ** Examples > > data(ppg) > data(mv1) > mv2<-calibexternal(mv1,ppg) Loading required package: modreg Warning: package 'modreg' has been merged into 'stats' > compare(mv1,mv2) > > > > cleanEx(); ..nameEx <- "calibexternal.massvectorlist" > > ### * calibexternal.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: calibexternal.massvectorlist > ### Title: External Calbiration > ### Aliases: calibexternal.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > data(ppg) > res <- calibexternal(mvl,ppg,getPPGmasses(),error=150) Loading required package: modreg Warning: package 'modreg' has been merged into 'stats' > > > > cleanEx(); ..nameEx <- "calibintstat" > > ### * calibintstat > > flush(stderr()); flush(stdout()) > > ### Name: calibintstat > ### Title: Constructor > ### Aliases: calibintstat > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(cal) > res<-getintcalib(mv1,cal,error=2,ppm=FALSE) > class(res) [1] "calibintstat" "calibstat" "lm" "mylistobj" > plot(res) > res<-getintcalib(mv1,cal,error=400,ppm=TRUE) > class(res) [1] "calibintstat" "calibstat" "lm" "mylistobj" > plot(res) > > > > cleanEx(); ..nameEx <- "caliblist" > > ### * caliblist > > flush(stderr()); flush(stdout()) > > ### Name: caliblist > ### Title: Constructor > ### Aliases: caliblist calibrelist calibintlist > ### Keywords: misc > > ### ** Examples > > #Example calibrelist class: > data(mvl) > mvl<-mvl[1:10] > res <- getrecalib(mvl) > print(res) Class : calibrelist Experiment : 020529r_dt_Pirellula Project : Calibstat List lenght : 10 Class calibstat object: calibrestat Fields in calibstat objects: info Coeff.Intercept Coeff.Slope lengthmv PQM tcoor > summary(res) $info [1] "020529r_dt_Pirellula" $summary lengthmv Coef.Intercept Coef.Slope PQM Min. : 8.00 Min. :-1.540e-01 Min. : 44.98 Min. : 7.704 1st Qu.:14.00 1st Qu.:-9.605e-02 1st Qu.:126.20 1st Qu.: 8.971 Median :23.50 Median :-1.667e-05 Median :207.44 Median : 9.674 Mean :23.80 Mean : 1.168e-02 Mean :267.97 Mean : 9.599 3rd Qu.:30.75 3rd Qu.: 1.328e-01 3rd Qu.:441.23 3rd Qu.:10.573 Max. :49.00 Max. : 1.883e-01 Max. :535.02 Max. :11.222 Xcoor Ycoor Min. :1 Min. : 1.00 1st Qu.:1 1st Qu.:11.25 Median :1 Median :13.50 Mean :1 Mean :12.70 3rd Qu.:1 3rd Qu.:15.75 Max. :1 Max. :18.00 > image(res,what="Coef.Intercept") > image(res,what="Coef.Slope") > plot(res) > hist(res) > dres<-as.data.frame(res) > plot(dres$Coef.Intercept,dres$PQM,xlab="Coef.Intercept",ylab="PQM") > #greate subset. > res2<-subset(res,PQM>10) > length(res2) [1] 4 > plot(res2) > test<-applyrecalib(mvl, res2) > > > > cleanEx(); ..nameEx <- "calibrestat" > > ### * calibrestat > > flush(stderr()); flush(stdout()) > > ### Name: calibrestat > ### Title: Constructor > ### Aliases: calibrestat > ### Keywords: misc > > ### ** Examples > > data(mv1) > res <- getrecalib(mv1) > print(res) class : calibrestat calibstat mylistobj info : 0_A1_1SRef lengthmv : 49 Coeff.Intercept : 0.05744198 Coeff.Slope : 44.97976 PQM : 11.22155 tcoor : 1 1 > as.vector(res) lengthmv Coef.Intercept Coef.Slope PQM Xcoor 49.00000000 0.05744198 44.97975911 11.22154876 1.00000000 Ycoor 1.00000000 > summary(res) info : 0_A1_1SRef lengthmv Coef.Intercept Coef.Slope PQM Xcoor 49.00000000 0.05744198 44.97975911 11.22154876 1.00000000 Ycoor 1.00000000 > image(res) Warning in image.mylistobj(res) : image not implemented for object of calss mylistobj! > plot(res) Warning in plot.calibstat(res) : Not implemented!! > > > > cleanEx(); ..nameEx <- "compare.massvector" > > ### * compare.massvector > > flush(stderr()); flush(stdout()) > > ### Name: compare.massvector > ### Title: Compares massvectors > ### Aliases: compare.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(mv2) > compare(mv1,mv2,error=5000,ppm=TRUE,uniq=TRUE) > compare(mv2,mv1,error=1,ppm=FALSE,uniq=TRUE) > > > > cleanEx(); ..nameEx <- "correctinternal.massvector" > > ### * correctinternal.massvector > > flush(stderr()); flush(stdout()) > > ### Name: correctinternal.massvector > ### Title: Internal Calibration > ### Aliases: correctinternal.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(cal) > res <- correctinternal(mv1,cal,error=200) > > > > cleanEx(); ..nameEx <- "correctinternal.massvectorlist" > > ### * correctinternal.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: correctinternal.massvectorlist > ### Title: Internal Calibration > ### Aliases: correctinternal.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > data(cal) > mvl2 <- correctinternal( mvl,cal, error=500 , ppm=TRUE ) > > > > cleanEx(); ..nameEx <- "diffFilter.massvector" > > ### * diffFilter.massvector > > flush(stderr()); flush(stdout()) > > ### Name: diffFilter.massvector > ### Title: Abundant Differences > ### Aliases: diffFilter.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > res<-getdiff(mv1,range=c(0,100)) > diffFilter(mv1,res,higher=TRUE) [1] info : (0_A1_1SRef) [1] coor : A=1 ; 1=1 mass area 1 842.4257 650.66 2 987.3931 180.30 3 1098.4314 3543.85 10 1466.5645 257.75 12 1672.7671 5067.09 24 1973.8298 1174.58 38 2465.0143 2196.50 40 2703.1986 1013.07 41 2811.1438 778.49 42 2914.3276 458.57 47 3331.4928 538.24 > diffFilter(mv1,res,higher=FALSE) [1] info : (0_A1_1SRef) [1] coor : A=1 ; 1=1 mass area 1 842.4257 650.66 2 987.3931 180.30 9 1296.6086 1528.91 11 1554.6257 600.61 23 1810.7358 4088.75 37 2312.9932 401.28 39 2505.0601 360.43 40 2703.1986 1013.07 41 2811.1438 778.49 46 3120.2176 273.91 49 3354.5540 415.73 > > > > cleanEx(); ..nameEx <- "diffFilter.massvectorlist" > > ### * diffFilter.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: diffFilter.massvectorlist > ### Title: Abundant Differences > ### Aliases: diffFilter.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > res<-getdiff(mvl,range=c(0,100)) > hist(res) > res<-gamasses(res,abund=100) > test<-diffFilter(mvl,res,higher=TRUE,error=0.1,uniq=TRUE) > test [1] Experiment : (020529r_dt_Pirellula) [1] Project : () [1] Nr (mv) : (100) > > > > cleanEx(); ..nameEx <- "experiment.mlist" > > ### * experiment.mlist > > flush(stderr()); flush(stdout()) > > ### Name: experiment.mlist > ### Title: Info Acces > ### Aliases: experiment.mlist info.mlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > experiment(mvl) [1] "020529r_dt_Pirellula" > mvl<-experiment(mvl,"newname") > > > > cleanEx(); ..nameEx <- "gamasses.massvector" > > ### * gamasses.massvector > > flush(stderr()); flush(stdout()) > > ### Name: gamasses.massvector > ### Title: Abundant masses > ### Aliases: gamasses.massvector > ### Keywords: misc > > ### ** Examples > > data(mvl) > mv<-unlist(mvl) > res<-gamasses(mv,abund=30,accur=0.3) > plot(res) > > > > cleanEx(); ..nameEx <- "gamasses.massvectorlist" > > ### * gamasses.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: gamasses.massvectorlist > ### Title: Abundant masses > ### Aliases: gamasses.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > #Filtering for abundant masses. > res<-gamasses(mvl,abund=50) > plot(res) > mvFilter(mvl[[1]],res) [1] info : (0_A1_1SRef) [1] coor : A=1 ; 1=1 mass area 2 987.3931 180.30 3 1098.4314 3543.85 4 1112.4456 251.17 5 1129.4501 345.22 6 1147.4617 2261.36 7 1207.5648 1948.22 8 1257.5929 204.77 9 1296.6086 1528.91 10 1466.5645 257.75 11 1554.6257 600.61 12 1672.7671 5067.09 13 1686.7343 863.64 14 1694.6771 4959.24 15 1712.7915 619.39 16 1734.7188 665.85 17 1746.7566 574.26 18 1750.6805 7579.83 19 1754.6996 2695.35 20 1766.7008 402.83 21 1793.7116 1784.45 22 1807.6837 604.98 23 1810.7358 4088.75 24 1973.8298 1174.58 25 2002.8374 504.87 26 2090.8222 15183.35 27 2104.8344 1877.67 28 2128.7796 467.04 29 2189.8599 594.90 30 2210.8834 4582.26 31 2224.9057 1765.44 32 2232.9109 931.45 33 2238.9288 491.35 34 2245.9799 1913.02 35 2248.8393 727.08 36 2298.9676 2394.62 37 2312.9932 401.28 38 2465.0143 2196.50 39 2505.0601 360.43 40 2703.1986 1013.07 41 2811.1438 778.49 42 2914.3276 458.57 43 3000.3723 8538.46 44 3014.3788 1666.68 45 3057.3808 395.89 46 3120.2176 273.91 47 3331.4928 538.24 48 3346.5022 2513.62 49 3354.5540 415.73 > res2<-mvFilter(mvl,res,abundant=TRUE) > image(res2,what="lengthmv") > image(mvl,what="lengthmv") > image(image(res2,what="lengthmv")/image(mvl,what="lengthmv")) > > hist(mvl,accur=0.3) > hist(res2,add=TRUE,col=2,accur=0.3) > > > > cleanEx(); ..nameEx <- "getPPGmasses" > > ### * getPPGmasses > > flush(stderr()); flush(stdout()) > > ### Name: getPPGmasses > ### Title: PPG masses > ### Aliases: getPPGmasses > ### Keywords: misc > > ### ** Examples > > plot(getPPGmasses(start=12,end=100)) > > > > cleanEx(); ..nameEx <- "getaccC" > > ### * getaccC > > flush(stderr()); flush(stdout()) > > ### Name: getaccC > ### Title: Find Matching Masses > ### Aliases: getaccC > ### Keywords: misc > > ### ** Examples > > getaccC(1001:1010,1001:1010,error=300,ppm=TRUE,uniq=TRUE) $plind [1] 1 2 3 4 5 6 7 8 9 10 $calind [1] 1 2 3 4 5 6 7 8 9 10 > > > > cleanEx(); ..nameEx <- "getdiff.massvectorlist" > > ### * getdiff.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: getdiff.massvectorlist > ### Title: Massdifferences > ### Aliases: getdiff.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > res<-getdiff(mvl,range=c(0,100)) > plot(res) > tt<-gamasses(res,abund=40) > plot(tt) > > > > cleanEx(); ..nameEx <- "getextcalib.massvector" > > ### * getextcalib.massvector > > flush(stderr()); flush(stdout()) > > ### Name: getextcalib.massvector > ### Title: External Error Model > ### Aliases: getextcalib.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(ppg) > res<-getextcalib(ppg[[1]]) Loading required package: modreg Warning: package 'modreg' has been merged into 'stats' > mv2 <- applycalib(res,mv1) > plot(mv1[,1],mv2[,1]-mv1[,1]) > > > > cleanEx(); ..nameEx <- "getglobalcalib.massvectorlist" > > ### * getglobalcalib.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: getglobalcalib.massvectorlist > ### Title: Set Based Internal Calbiration > ### Aliases: getglobalcalib.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > data(cal) > res<-getglobalcalib(mvl,cal,error=500,ppm=TRUE) > hist(res) > > > > cleanEx(); ..nameEx <- "getintcalib.massvectorlist" > > ### * getintcalib.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: getintcalib.massvectorlist > ### Title: Internal Calbiration > ### Aliases: getintcalib.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > data(cal) > res<-getintcalib(mvl,cal,error=400,ppm=TRUE) > plot(res) > > > > cleanEx(); ..nameEx <- "getrecalib.massvector" > > ### * getrecalib.massvector > > flush(stderr()); flush(stdout()) > > ### Name: getrecalib.massvector > ### Title: Precalibration > ### Aliases: getrecalib.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > res <- getrecalib(mv1) > print(res) class : calibrestat calibstat mylistobj info : 0_A1_1SRef lengthmv : 49 Coeff.Intercept : 0.05744198 Coeff.Slope : 44.97976 PQM : 11.22155 tcoor : 1 1 > as.vector(res) lengthmv Coef.Intercept Coef.Slope PQM Xcoor 49.00000000 0.05744198 44.97975911 11.22154876 1.00000000 Ycoor 1.00000000 > summary(res) info : 0_A1_1SRef lengthmv Coef.Intercept Coef.Slope PQM Xcoor 49.00000000 0.05744198 44.97975911 11.22154876 1.00000000 Ycoor 1.00000000 > image(res) Warning in image.mylistobj(res) : image not implemented for object of calss mylistobj! > plot(res) Warning in plot.calibstat(res) : Not implemented!! > > > > cleanEx(); ..nameEx <- "getrecalib.massvectorlist" > > ### * getrecalib.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: getrecalib.massvectorlist > ### Title: Precalibration > ### Aliases: getrecalib.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > mvl<-mvl[1:100] > res <- getrecalib(mvl) > print(res) Class : calibrelist Experiment : 020529r_dt_Pirellula Project : Calibstat List lenght : 100 Class calibstat object: calibrestat Fields in calibstat objects: info Coeff.Intercept Coeff.Slope lengthmv PQM tcoor > summary(res) $info [1] "020529r_dt_Pirellula" $summary lengthmv Coef.Intercept Coef.Slope PQM Min. : 8.00 Min. :-0.25008 Min. :-114.93 Min. : 7.704 1st Qu.:25.00 1st Qu.:-0.10422 1st Qu.: 28.74 1st Qu.:10.270 Median :33.50 Median :-0.07850 Median : 84.97 Median :10.666 Mean :37.03 Mean :-0.05974 Mean : 122.92 Mean :10.536 3rd Qu.:49.25 3rd Qu.:-0.02094 3rd Qu.: 181.19 3rd Qu.:11.035 Max. :81.00 Max. : 0.22554 Max. : 560.04 Max. :11.990 Xcoor Ycoor Min. :1.00 Min. : 1.00 1st Qu.:2.00 1st Qu.: 6.00 Median :3.00 Median :12.00 Mean :2.84 Mean :12.06 3rd Qu.:4.00 3rd Qu.:18.00 Max. :5.00 Max. :24.00 > image(res,what="Coef.Intercept") > image(res,what="Coef.Slope") > plot(res) > hist(res) > dres<-as.data.frame(res) > plot(dres$Coef.Intercept,dres$PQM,xlab="Coef.Intercept",ylab="PQM") > #create subset. > res2<-subset(res,PQM>10) > length(res2) [1] 80 > plot(res2) > test<-applyrecalib(mvl, res2) > plot(test) > > > > cleanEx(); ..nameEx <- "globalcalib.massvectorlist" > > ### * globalcalib.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: globalcalib.massvectorlist > ### Title: Set Based Internal Calibration > ### Aliases: globalcalib.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > data(cal) > mvl2<-globalcalib(mvl,cal,error=500,labund=12) [1] info : (020529r_dt_Pirellula_abundant) [1] coor : ; mass number wm 1 758.3425 54 758.3904 2 842.4669 83 842.5143 3 870.4893 34 870.5184 4 1045.5140 47 1045.5243 5 1296.6577 88 1296.6573 6 1657.9310 25 1657.9684 7 1672.8609 78 1672.8953 8 1710.8678 26 1710.8434 9 1712.8778 70 1712.8999 10 1940.8357 30 1940.8434 11 2082.8633 33 2082.8434 12 2211.0140 68 2211.0277 13 2225.0274 67 2225.0315 14 2233.0180 52 2233.0291 15 2239.0235 36 2239.0321 16 2246.0617 57 2246.0417 17 2249.0114 45 2249.0281 18 2299.0433 44 2299.0343 19 2465.1551 67 2465.1559 20 2505.1815 47 2505.1634 21 3346.7026 31 3346.7184 [1] info : (020529r_dt_Pirellula_abundant) [1] coor : ; mass number wm 4 1045.5140 47 1045.5243 20 2505.1815 47 2505.1634 14 2233.0180 52 2233.0291 1 758.3425 54 758.3904 16 2246.0617 57 2246.0417 13 2225.0274 67 2225.0315 19 2465.1551 67 2465.1559 12 2211.0140 68 2211.0277 9 1712.8778 70 1712.8999 7 1672.8609 78 1672.8953 2 842.4669 83 842.5143 5 1296.6577 88 1296.6573 > > > > cleanEx(); ..nameEx <- "hist.calibintlist" > > ### * hist.calibintlist > > flush(stderr()); flush(stdout()) > > ### Name: hist.calibintlist > ### Title: Histogram Plot > ### Aliases: hist.calibintlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > data(cal) > mvl <- mvl[1:100] > data(cal) > ires <- getintcalib(mvl,cal,error=250) > hist(ires) > > > > cleanEx(); ..nameEx <- "hist.calibrelist" > > ### * hist.calibrelist > > flush(stderr()); flush(stdout()) > > ### Name: hist.calibrelist > ### Title: Histogram Plot > ### Aliases: hist.calibrelist > ### Keywords: misc > > ### ** Examples > > data(mvl) > mvl<-mvl[1:100] > res2 <- getrecalib(mvl) # get recalibration model for not filtered data > hist(res2) > > > > cleanEx(); ..nameEx <- "hist.massvector" > > ### * hist.massvector > > flush(stderr()); flush(stdout()) > > ### Name: hist.massvector > ### Title: Histograms > ### Aliases: hist.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > hist(mv1) > > > > cleanEx(); ..nameEx <- "hist.massvectorlist" > > ### * hist.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: hist.massvectorlist > ### Title: Histograms > ### Aliases: hist.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > hist(mvl) > > > > cleanEx(); ..nameEx <- "image.massvector" > > ### * image.massvector > > flush(stderr()); flush(stdout()) > > ### Name: image.massvector > ### Title: Display a Color Image > ### Aliases: image.massvector > ### Keywords: misc > > ### ** Examples > > data(mv2) > data(mv1) > image(mv1,mv2) > image(mv1,mv2,error=500) > > > > cleanEx(); ..nameEx <- "image.mlist" > > ### * image.mlist > > flush(stderr()); flush(stdout()) > > ### Name: image.mlist > ### Title: Display a Color Image > ### Aliases: image.mlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > image(mvl,what="lengthmv") > > > > cleanEx(); ..nameEx <- "info.mylistobj" > > ### * info.mylistobj > > flush(stderr()); flush(stdout()) > > ### Name: info.mylistobj > ### Title: Info Acces > ### Aliases: info.mylistobj > ### Keywords: misc > > ### ** Examples > > data(mv1) > res <- getrecalib(mv1) > info(res) [1] "0_A1_1SRef" > res<-info(res,"testname") > > > > cleanEx(); ..nameEx <- "info.myobj" > > ### * info.myobj > > flush(stderr()); flush(stdout()) > > ### Name: info.myobj > ### Title: Info Acces > ### Aliases: info.myobj > ### Keywords: misc > > ### ** Examples > > data(mv1) > info(mv1) [1] "0_A1_1SRef" > mv1<-info(mv1,"testname") > > > > cleanEx(); ..nameEx <- "length.massvector" > > ### * length.massvector > > flush(stderr()); flush(stdout()) > > ### Name: length.massvector > ### Title: Length of Massvector > ### Aliases: length.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > length(mv1) [1] 49 > > > > cleanEx(); ..nameEx <- "mass.massvector" > > ### * mass.massvector > > flush(stderr()); flush(stdout()) > > ### Name: mass.massvector > ### Title: Mass Access. > ### Aliases: mass.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > mass(mv1) 1 2 3 4 5 6 7 8 842.4257 987.3931 1098.4314 1112.4456 1129.4501 1147.4617 1207.5648 1257.5929 9 10 11 12 13 14 15 16 1296.6086 1466.5645 1554.6257 1672.7671 1686.7343 1694.6771 1712.7915 1734.7188 17 18 19 20 21 22 23 24 1746.7566 1750.6805 1754.6996 1766.7008 1793.7116 1807.6837 1810.7358 1973.8298 25 26 27 28 29 30 31 32 2002.8374 2090.8222 2104.8344 2128.7796 2189.8599 2210.8834 2224.9057 2232.9109 33 34 35 36 37 38 39 40 2238.9288 2245.9799 2248.8393 2298.9676 2312.9932 2465.0143 2505.0601 2703.1986 41 42 43 44 45 46 47 48 2811.1438 2914.3276 3000.3723 3014.3788 3057.3808 3120.2176 3331.4928 3346.5022 49 3354.5540 > mass(mv1,1:10) [,1] [,2] [1,] 1 1 [2,] 2 1 [3,] 3 1 [4,] 4 1 [5,] 5 1 [6,] 6 1 [7,] 7 1 [8,] 8 1 [9,] 9 1 [10,] 10 1 > > > > cleanEx(); ..nameEx <- "massvector" > > ### * massvector > > flush(stderr()); flush(stdout()) > > ### Name: massvector > ### Title: Constructor > ### Aliases: massvector > ### Keywords: misc > > ### ** Examples > > massvector("hello march",NULL) [1] info : (hello march) [1] coor : ; mass C1 > massvector("hello march",1:100) [1] info : (hello march) [1] coor : ; mass C2 1 1 1 2 2 1 3 3 1 4 4 1 5 5 1 6 6 1 7 7 1 8 8 1 9 9 1 10 10 1 11 11 1 12 12 1 13 13 1 14 14 1 15 15 1 16 16 1 17 17 1 18 18 1 19 19 1 20 20 1 21 21 1 22 22 1 23 23 1 24 24 1 25 25 1 26 26 1 27 27 1 28 28 1 29 29 1 30 30 1 31 31 1 32 32 1 33 33 1 34 34 1 35 35 1 36 36 1 37 37 1 38 38 1 39 39 1 40 40 1 41 41 1 42 42 1 43 43 1 44 44 1 45 45 1 46 46 1 47 47 1 48 48 1 49 49 1 50 50 1 51 51 1 52 52 1 53 53 1 54 54 1 55 55 1 56 56 1 57 57 1 58 58 1 59 59 1 60 60 1 61 61 1 62 62 1 63 63 1 64 64 1 65 65 1 66 66 1 67 67 1 68 68 1 69 69 1 70 70 1 71 71 1 72 72 1 73 73 1 74 74 1 75 75 1 76 76 1 77 77 1 78 78 1 79 79 1 80 80 1 81 81 1 82 82 1 83 83 1 84 84 1 85 85 1 86 86 1 87 87 1 88 88 1 89 89 1 90 90 1 91 91 1 92 92 1 93 93 1 94 94 1 95 95 1 96 96 1 97 97 1 98 98 1 99 99 1 100 100 1 > massvector("hello march",cbind(1:10,10:1)) [1] info : (hello march) [1] coor : ; mass C2 1 1 10 2 2 9 3 3 8 4 4 7 5 5 6 6 6 5 7 7 4 8 8 3 9 9 2 10 10 1 > tmp<-cbind(1:10,1:10) > colnames(tmp)<-c("mass","test") > rr<-massvector("hello march",tmp) > rr2<-massvector("hello bart",cbind(1:12,1:12)) > # plot functions for massvector > plot(rr) > hist(rr) > summary(rr) $lengthmv [1] 10 $mass Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 $test Min. 1st Qu. Median Mean 3rd Qu. Max. 1 1 1 1 1 1 > image(rr) > info(rr) [1] "hello march" > # setting new masses > mass(rr) 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10 > mass(rr,1:10) [,1] [,2] [1,] 1 1 [2,] 2 1 [3,] 3 1 [4,] 4 1 [5,] 5 1 [6,] 6 1 [7,] 7 1 [8,] 8 1 [9,] 9 1 [10,] 10 1 > peaks(rr,cbind(1:10,11:20)) [1] info : (hello march) [1] coor : ; mass C2 1 1 11 2 2 12 3 3 13 4 4 14 5 5 15 6 6 16 7 7 17 8 8 18 9 9 19 10 10 20 > # plotting with masses > data(mv1) > data(mv2) > plot(mv1,mv2) > image(mv1 ,mv2) > summary(mv1) $lengthmv [1] 49 $mass Min. 1st Qu. Median Mean 3rd Qu. Max. 842.4 842.4 842.4 842.4 842.4 842.4 $area Min. 1st Qu. Median Mean 3rd Qu. Max. 650.7 650.7 650.7 650.7 650.7 650.7 > print(mv1) [1] info : (0_A1_1SRef) [1] coor : A=1 ; 1=1 mass area 1 842.4257 650.66 2 987.3931 180.30 3 1098.4314 3543.85 4 1112.4456 251.17 5 1129.4501 345.22 6 1147.4617 2261.36 7 1207.5648 1948.22 8 1257.5929 204.77 9 1296.6086 1528.91 10 1466.5645 257.75 11 1554.6257 600.61 12 1672.7671 5067.09 13 1686.7343 863.64 14 1694.6771 4959.24 15 1712.7915 619.39 16 1734.7188 665.85 17 1746.7566 574.26 18 1750.6805 7579.83 19 1754.6996 2695.35 20 1766.7008 402.83 21 1793.7116 1784.45 22 1807.6837 604.98 23 1810.7358 4088.75 24 1973.8298 1174.58 25 2002.8374 504.87 26 2090.8222 15183.35 27 2104.8344 1877.67 28 2128.7796 467.04 29 2189.8599 594.90 30 2210.8834 4582.26 31 2224.9057 1765.44 32 2232.9109 931.45 33 2238.9288 491.35 34 2245.9799 1913.02 35 2248.8393 727.08 36 2298.9676 2394.62 37 2312.9932 401.28 38 2465.0143 2196.50 39 2505.0601 360.43 40 2703.1986 1013.07 41 2811.1438 778.49 42 2914.3276 458.57 43 3000.3723 8538.46 44 3014.3788 1666.68 45 3057.3808 395.89 46 3120.2176 273.91 47 3331.4928 538.24 48 3346.5022 2513.62 49 3354.5540 415.73 > hist(mv1) > plot(mv1) > image(mv1,mv2,error=199,ppm=FALSE) > > > > cleanEx(); ..nameEx <- "massvectorlist" > > ### * massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: massvectorlist > ### Title: Constructor > ### Aliases: massvectorlist > ### Keywords: misc > > ### ** Examples > > # testing constructor. > massvectorlist("my1experiment") [1] Experiment : (my1experiment) [1] Project : () [1] Nr (mv) : (0) > data(mvl) > massvectorlist("my2experiment",mvl,"hello project") [1] Experiment : (my2experiment) [1] Project : (hello project) [1] Nr (mv) : (100) > plot(mvl) > summary(mvl) $info [1] "020529r_dt_Pirellula" $summary lengthmv mass.Min. mass.1st.Qu. mass.Median Min. : 8.00 Min. : 750.3 Min. : 750.3 Min. : 750.3 1st Qu.:25.00 1st Qu.: 758.4 1st Qu.: 758.4 1st Qu.: 758.4 Median :33.50 Median : 758.4 Median : 758.4 Median : 758.4 Mean :37.03 Mean : 804.5 Mean : 804.5 Mean : 804.5 3rd Qu.:49.25 3rd Qu.: 842.4 3rd Qu.: 842.4 3rd Qu.: 842.4 Max. :81.00 Max. :1296.0 Max. :1296.0 Max. :1296.0 mass.Mean mass.3rd.Qu. mass.Max. area.Min. Min. : 750.3 Min. : 750.3 Min. : 750.3 Min. : 74.43 1st Qu.: 758.4 1st Qu.: 758.4 1st Qu.: 758.4 1st Qu.: 152.75 Median : 758.4 Median : 758.4 Median : 758.4 Median : 212.60 Mean : 804.5 Mean : 804.5 Mean : 804.5 Mean : 335.21 3rd Qu.: 842.4 3rd Qu.: 842.4 3rd Qu.: 842.4 3rd Qu.: 301.18 Max. :1296.0 Max. :1296.0 Max. :1296.0 Max. :2780.00 area.1st.Qu. area.Median area.Mean area.3rd.Qu. Min. : 74.43 Min. : 74.43 Min. : 74.43 Min. : 74.43 1st Qu.: 152.75 1st Qu.: 152.75 1st Qu.: 152.75 1st Qu.: 152.75 Median : 212.60 Median : 212.60 Median : 212.60 Median : 212.60 Mean : 335.21 Mean : 335.21 Mean : 335.21 Mean : 335.21 3rd Qu.: 301.18 3rd Qu.: 301.18 3rd Qu.: 301.18 3rd Qu.: 301.18 Max. :2780.00 Max. :2780.00 Max. :2780.00 Max. :2780.00 area.Max. Min. : 74.43 1st Qu.: 152.75 Median : 212.60 Mean : 335.21 3rd Qu.: 301.18 Max. :2780.00 > hist(mvl) > hist(mvl) > image(mvl,what="lengthmv") > mvl2<-mvl[1:100] > plot(mvl2) > summary(mvl2) $info [1] "020529r_dt_Pirellula" $summary lengthmv mass.Min. mass.1st.Qu. mass.Median Min. : 8.00 Min. : 750.3 Min. : 750.3 Min. : 750.3 1st Qu.:25.00 1st Qu.: 758.4 1st Qu.: 758.4 1st Qu.: 758.4 Median :33.50 Median : 758.4 Median : 758.4 Median : 758.4 Mean :37.03 Mean : 804.5 Mean : 804.5 Mean : 804.5 3rd Qu.:49.25 3rd Qu.: 842.4 3rd Qu.: 842.4 3rd Qu.: 842.4 Max. :81.00 Max. :1296.0 Max. :1296.0 Max. :1296.0 mass.Mean mass.3rd.Qu. mass.Max. area.Min. Min. : 750.3 Min. : 750.3 Min. : 750.3 Min. : 74.43 1st Qu.: 758.4 1st Qu.: 758.4 1st Qu.: 758.4 1st Qu.: 152.75 Median : 758.4 Median : 758.4 Median : 758.4 Median : 212.60 Mean : 804.5 Mean : 804.5 Mean : 804.5 Mean : 335.21 3rd Qu.: 842.4 3rd Qu.: 842.4 3rd Qu.: 842.4 3rd Qu.: 301.18 Max. :1296.0 Max. :1296.0 Max. :1296.0 Max. :2780.00 area.1st.Qu. area.Median area.Mean area.3rd.Qu. Min. : 74.43 Min. : 74.43 Min. : 74.43 Min. : 74.43 1st Qu.: 152.75 1st Qu.: 152.75 1st Qu.: 152.75 1st Qu.: 152.75 Median : 212.60 Median : 212.60 Median : 212.60 Median : 212.60 Mean : 335.21 Mean : 335.21 Mean : 335.21 Mean : 335.21 3rd Qu.: 301.18 3rd Qu.: 301.18 3rd Qu.: 301.18 3rd Qu.: 301.18 Max. :2780.00 Max. :2780.00 Max. :2780.00 Max. :2780.00 area.Max. Min. : 74.43 1st Qu.: 152.75 Median : 212.60 Mean : 335.21 3rd Qu.: 301.18 Max. :2780.00 > hist(mvl2) > image(mvl2,what="lengthmv") > #testing assingments > mvl2[[11]]<-mvl2[[1]] > plot(mvl2[[11]],mvl2[[1]]) > image(mvl2[[11]],mvl2[[1]]) > #make one massvector out of the peaklist > tt<-unlist(mvl) > plot(tt) > > > > cleanEx(); ..nameEx <- "mget.massvector" > > ### * mget.massvector > > flush(stderr()); flush(stdout()) > > ### Name: mget.massvector > ### Title: Field Access > ### Aliases: mget.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > mget(mv1,"info") [1] "0_A1_1SRef" > mget(mv1,"peaks") mass area 1 842.4257 650.66 2 987.3931 180.30 3 1098.4314 3543.85 4 1112.4456 251.17 5 1129.4501 345.22 6 1147.4617 2261.36 7 1207.5648 1948.22 8 1257.5929 204.77 9 1296.6086 1528.91 10 1466.5645 257.75 11 1554.6257 600.61 12 1672.7671 5067.09 13 1686.7343 863.64 14 1694.6771 4959.24 15 1712.7915 619.39 16 1734.7188 665.85 17 1746.7566 574.26 18 1750.6805 7579.83 19 1754.6996 2695.35 20 1766.7008 402.83 21 1793.7116 1784.45 22 1807.6837 604.98 23 1810.7358 4088.75 24 1973.8298 1174.58 25 2002.8374 504.87 26 2090.8222 15183.35 27 2104.8344 1877.67 28 2128.7796 467.04 29 2189.8599 594.90 30 2210.8834 4582.26 31 2224.9057 1765.44 32 2232.9109 931.45 33 2238.9288 491.35 34 2245.9799 1913.02 35 2248.8393 727.08 36 2298.9676 2394.62 37 2312.9932 401.28 38 2465.0143 2196.50 39 2505.0601 360.43 40 2703.1986 1013.07 41 2811.1438 778.49 42 2914.3276 458.57 43 3000.3723 8538.46 44 3014.3788 1666.68 45 3057.3808 395.89 46 3120.2176 273.91 47 3331.4928 538.24 48 3346.5022 2513.62 49 3354.5540 415.73 > > > > cleanEx(); ..nameEx <- "mget.mlist" > > ### * mget.mlist > > flush(stderr()); flush(stdout()) > > ### Name: mget.mlist > ### Title: Field Access > ### Aliases: mget.mlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > mget(mvl) [1] "data" "experiment" "project" > mget(mvl,"info") Warning in mget.myobj(mvl, "info") : info not in the attributes list :data experiment project > mget(mvl,"tcoor") $coorX A A A A A A A A A A A A A A A A A A A A A A A A B B B B B B B B B B B B B B B B 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 B B C C C C C C C C C C C C C C C C C C C C C C C C D D D D D D D D D D D D D D 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 4 4 4 4 D D D D E E E E E E E E E E E E E E E E 4 4 4 4 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 $coorY 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 23 24 3 4 5 6 7 8 9 1 10 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 23 24 3 4 5 6 7 8 9 1 10 11 12 13 15 17 19 2 21 23 3 4 5 6 7 8 9 1 10 11 12 13 14 15 16 17 18 11 12 13 15 17 19 2 21 23 3 4 5 6 7 8 9 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 23 24 3 4 5 6 7 8 9 1 10 11 12 13 15 17 19 2 21 23 3 19 2 20 21 22 23 24 3 4 5 6 7 8 9 1 10 11 12 13 15 17 19 2 21 23 3 4 5 6 7 8 9 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 23 4 5 6 7 8 9 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 23 > > > > cleanEx(); ..nameEx <- "mget.mylistobj" > > ### * mget.mylistobj > > flush(stderr()); flush(stdout()) > > ### Name: mget.mylistobj > ### Title: Field Access > ### Aliases: mget.mylistobj > ### Keywords: misc > > ### ** Examples > > data(mv1) > res <- getrecalib(mv1) > class(res) [1] "calibrestat" "calibstat" "mylistobj" > mget(mv1,"lenghtmv") Warning in mget.myobj(mv1, "lenghtmv") : lenghtmv not in the attributes list :info tcoor > mget(mv1,"Coef.Intercept") Warning in mget.myobj(mv1, "Coef.Intercept") : Coef.Intercept not in the attributes list :info tcoor > > > > cleanEx(); ..nameEx <- "mget.myobj" > > ### * mget.myobj > > flush(stderr()); flush(stdout()) > > ### Name: mget.myobj > ### Title: Field Access > ### Aliases: mget.myobj > ### Keywords: misc > > ### ** Examples > > data(mv1) > mget(mv1) [1] "info" "tcoor" > mget(mv1,"info") [1] "0_A1_1SRef" > > > > cleanEx(); ..nameEx <- "mvFilter.massvector" > > ### * mvFilter.massvector > > flush(stderr()); flush(stdout()) > > ### Name: mvFilter.massvector > ### Title: Filtering Massvector > ### Aliases: mvFilter.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(mv2) > mvFilter(mv1,mv2,error=250,match=FALSE) [1] info : (0_A1_1SRef) [1] coor : A=1 ; 1=1 mass area 2 987.3931 180.30 3 1098.4314 3543.85 4 1112.4456 251.17 5 1129.4501 345.22 6 1147.4617 2261.36 7 1207.5648 1948.22 8 1257.5929 204.77 10 1466.5645 257.75 11 1554.6257 600.61 13 1686.7343 863.64 16 1734.7188 665.85 17 1746.7566 574.26 18 1750.6805 7579.83 19 1754.6996 2695.35 20 1766.7008 402.83 21 1793.7116 1784.45 22 1807.6837 604.98 23 1810.7358 4088.75 24 1973.8298 1174.58 25 2002.8374 504.87 26 2090.8222 15183.35 27 2104.8344 1877.67 28 2128.7796 467.04 29 2189.8599 594.90 37 2312.9932 401.28 40 2703.1986 1013.07 41 2811.1438 778.49 42 2914.3276 458.57 43 3000.3723 8538.46 44 3014.3788 1666.68 45 3057.3808 395.89 46 3120.2176 273.91 47 3331.4928 538.24 49 3354.5540 415.73 > mvFilter(mv1,mv2,error=250,match=TRUE) [1] info : (0_A1_1SRef) [1] coor : A=1 ; 1=1 mass area 1 842.4257 650.66 9 1296.6086 1528.91 12 1672.7671 5067.09 14 1694.6771 4959.24 15 1712.7915 619.39 30 2210.8834 4582.26 31 2224.9057 1765.44 32 2232.9109 931.45 33 2238.9288 491.35 34 2245.9799 1913.02 35 2248.8393 727.08 36 2298.9676 2394.62 38 2465.0143 2196.50 39 2505.0601 360.43 48 3346.5022 2513.62 > > > > cleanEx(); ..nameEx <- "mvFilter.massvectorlist" > > ### * mvFilter.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: mvFilter.massvectorlist > ### Title: Filtering Massvector > ### Aliases: mvFilter.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > mvl<-mvFilter(mvl,mvl[[1]],match=FALSE,error=250) > length(mvl[[1]]) [1] 0 > > > > cleanEx(); ..nameEx <- "peaks.massvector" > > ### * peaks.massvector > > flush(stderr()); flush(stdout()) > > ### Name: peaks.massvector > ### Title: Data Access > ### Aliases: peaks.massvector > ### Keywords: misc > > ### ** Examples > > mv1<-massvector() > mv1<- peaks(mv1,cbind(1:10,1:10)) > peaks(mv1) mass C2 1 1 1 2 2 2 3 3 3 4 4 4 5 5 5 6 6 6 7 7 7 8 8 8 9 9 9 10 10 10 > > > > cleanEx(); ..nameEx <- "plot.calibintlist" > > ### * plot.calibintlist > > flush(stderr()); flush(stdout()) > > ### Name: plot.calibintlist > ### Title: Calibintlist Plotting > ### Aliases: plot.calibintlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > data(cal) > mvl <- mvl[1:100] > ires <- getintcalib(mvl,cal,error=250) > plot(ires) > > > > cleanEx(); ..nameEx <- "plot.calibintstat" > > ### * plot.calibintstat > > flush(stderr()); flush(stdout()) > > ### Name: plot.calibintstat > ### Title: Calibinstat Plotting > ### Aliases: plot.calibintstat > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(cal) > res<-getintcalib(mv1,cal,error=500,ppm=TRUE) > plot(res) > > > > cleanEx(); ..nameEx <- "plot.calibrelist" > > ### * plot.calibrelist > > flush(stderr()); flush(stdout()) > > ### Name: plot.calibrelist > ### Title: Plot > ### Aliases: plot.calibrelist > ### Keywords: misc > > ### ** Examples > > data(mvl) > mvl<-mvl[1:100] > res2 <- getrecalib(mvl) # get recalibration model for not filtered data > plot(res2) > > > > cleanEx(); ..nameEx <- "plot.calibspline" > > ### * plot.calibspline > > flush(stderr()); flush(stdout()) > > ### Name: plot.calibspline > ### Title: Calibspline Plotting > ### Aliases: plot.calibspline > ### Keywords: misc > > ### ** Examples > > data(ppg) > tmp <- getextcalib(ppg,error=200) Loading required package: modreg Warning: package 'modreg' has been merged into 'stats' > plot(tmp) > > > > cleanEx(); ..nameEx <- "plot.massvector" > > ### * plot.massvector > > flush(stderr()); flush(stdout()) > > ### Name: plot.massvector > ### Title: Massvector Plotting > ### Aliases: plot.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(mv2) > plot(mv1) > plot(mv1,mv2) > > > > cleanEx(); ..nameEx <- "plot.massvectorlist" > > ### * plot.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: plot.massvectorlist > ### Title: Massvectorlist Plotting > ### Aliases: plot.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > plot(mvl,col= 3 ) > tt<- gamasses(mvl,abund=50) > plot(mvl,col=1, xlim=c(tt[1,1]-0.4,tt[1,1]+0.4)) > > > > cleanEx(); ..nameEx <- "print.calibintstat" > > ### * print.calibintstat > > flush(stderr()); flush(stdout()) > > ### Name: print.calibintstat > ### Title: Print calibintstat > ### Aliases: print.calibintstat > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(cal) > res<-getintcalib(mv1,cal,error=500,ppm=TRUE) > print(res) info : 0_A1_1SRef type : ppm Intercept : 98.17174 Slope : -65.9618 Length pl : 49 nr match : 9 tcoor : 1 1 > > > > cleanEx(); ..nameEx <- "print.caliblist" > > ### * print.caliblist > > flush(stderr()); flush(stdout()) > > ### Name: print.caliblist > ### Title: Print caliblist > ### Aliases: print.caliblist > ### Keywords: misc > > ### ** Examples > > data(mvl) > mvl<-mvl[1:100] > data(cal) > test <- getintcalib(mvl,cal,error=500) > print(test) Class : calibintlist Experiment : 020529r_dt_Pirellula Project : Calibstat List lenght : 100 Class calibstat object: calibintstat Fields in calibstat objects: info Coeff.Intercept Coeff.Slope info lengthmv nrmatch ppm tcoor > > > > cleanEx(); ..nameEx <- "print.calibrestat" > > ### * print.calibrestat > > flush(stderr()); flush(stdout()) > > ### Name: print.calibrestat > ### Title: Print Calibrestat Object > ### Aliases: print.calibrestat > ### Keywords: misc > > ### ** Examples > > data(mv1) > res<-getrecalib(mv1) > print(res) class : calibrestat calibstat mylistobj info : 0_A1_1SRef lengthmv : 49 Coeff.Intercept : 0.05744198 Coeff.Slope : 44.97976 PQM : 11.22155 tcoor : 1 1 > > > > cleanEx(); ..nameEx <- "print.calibspline" > > ### * print.calibspline > > flush(stderr()); flush(stdout()) > > ### Name: print.calibspline > ### Title: Print Calibspline Object > ### Aliases: print.calibspline > ### Keywords: misc > > ### ** Examples > > data(ppg) > tmp <- getextcalib(ppg,error=200) Loading required package: modreg Warning: package 'modreg' has been merged into 'stats' > print(tmp) info : 020529r_dt_Pirellula_ppg Call: smooth.spline(x = theo, y = error) Smoothing Parameter spar= 0.3575599 lambda= 2.501043e-05 (13 iterations) Equivalent Degrees of Freedom (Df): 26.03541 Penalized Criterion: 209.0687 GCV: 8.499507 > > > > cleanEx(); ..nameEx <- "print.massvector" > > ### * print.massvector > > flush(stderr()); flush(stdout()) > > ### Name: print.massvector > ### Title: Print massvector > ### Aliases: print.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > print(mv1) [1] info : (0_A1_1SRef) [1] coor : A=1 ; 1=1 mass area 1 842.4257 650.66 2 987.3931 180.30 3 1098.4314 3543.85 4 1112.4456 251.17 5 1129.4501 345.22 6 1147.4617 2261.36 7 1207.5648 1948.22 8 1257.5929 204.77 9 1296.6086 1528.91 10 1466.5645 257.75 11 1554.6257 600.61 12 1672.7671 5067.09 13 1686.7343 863.64 14 1694.6771 4959.24 15 1712.7915 619.39 16 1734.7188 665.85 17 1746.7566 574.26 18 1750.6805 7579.83 19 1754.6996 2695.35 20 1766.7008 402.83 21 1793.7116 1784.45 22 1807.6837 604.98 23 1810.7358 4088.75 24 1973.8298 1174.58 25 2002.8374 504.87 26 2090.8222 15183.35 27 2104.8344 1877.67 28 2128.7796 467.04 29 2189.8599 594.90 30 2210.8834 4582.26 31 2224.9057 1765.44 32 2232.9109 931.45 33 2238.9288 491.35 34 2245.9799 1913.02 35 2248.8393 727.08 36 2298.9676 2394.62 37 2312.9932 401.28 38 2465.0143 2196.50 39 2505.0601 360.43 40 2703.1986 1013.07 41 2811.1438 778.49 42 2914.3276 458.57 43 3000.3723 8538.46 44 3014.3788 1666.68 45 3057.3808 395.89 46 3120.2176 273.91 47 3331.4928 538.24 48 3346.5022 2513.62 49 3354.5540 415.73 > > > > cleanEx(); ..nameEx <- "print.massvectorlist" > > ### * print.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: print.massvectorlist > ### Title: Print massvectorlist > ### Aliases: print.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > print(mvl) [1] Experiment : (020529r_dt_Pirellula) [1] Project : () [1] Nr (mv) : (100) > > > > cleanEx(); ..nameEx <- "project.massvectorlist" > > ### * project.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: project.massvectorlist > ### Title: Acces > ### Aliases: project.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > project(mvl) NULL > mvl <- project(mvl,"newprojectname") > > > > cleanEx(); ..nameEx <- "readF.massvector" > > ### * readF.massvector > > flush(stderr()); flush(stdout()) > > ### Name: readF.massvector > ### Title: Read Massvector > ### Aliases: readF.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > writeF(mv1,".") > readF(massvector(info(mv1)),".") [1] info : (0_A1_1SRef) [1] coor : 1 ; 1 mass C2 1 842.4257 650.66 2 987.3931 180.30 3 1098.4314 3543.85 4 1112.4456 251.17 5 1129.4501 345.22 6 1147.4617 2261.36 7 1207.5648 1948.22 8 1257.5929 204.77 9 1296.6086 1528.91 10 1466.5645 257.75 11 1554.6257 600.61 12 1672.7671 5067.09 13 1686.7343 863.64 14 1694.6771 4959.24 15 1712.7915 619.39 16 1734.7188 665.85 17 1746.7566 574.26 18 1750.6805 7579.83 19 1754.6996 2695.35 20 1766.7008 402.83 21 1793.7116 1784.45 22 1807.6837 604.98 23 1810.7358 4088.75 24 1973.8298 1174.58 25 2002.8374 504.87 26 2090.8222 15183.35 27 2104.8344 1877.67 28 2128.7796 467.04 29 2189.8599 594.90 30 2210.8834 4582.26 31 2224.9057 1765.44 32 2232.9109 931.45 33 2238.9288 491.35 34 2245.9799 1913.02 35 2248.8393 727.08 36 2298.9676 2394.62 37 2312.9932 401.28 38 2465.0143 2196.50 39 2505.0601 360.43 40 2703.1986 1013.07 41 2811.1438 778.49 42 2914.3276 458.57 43 3000.3723 8538.46 44 3014.3788 1666.68 45 3057.3808 395.89 46 3120.2176 273.91 47 3331.4928 538.24 48 3346.5022 2513.62 49 3354.5540 415.73 > file.remove(paste(info(mv1),".txt",sep="")) [1] TRUE > > > > cleanEx(); ..nameEx <- "readF.massvectorlist" > > ### * readF.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: readF.massvectorlist > ### Title: Reads massvectorlist > ### Aliases: readF.massvectorlist > ### Keywords: misc > > ### ** Examples > > data( mvl ) > mvl [1] Experiment : (020529r_dt_Pirellula) [1] Project : () [1] Nr (mv) : (100) > writeF( mvl , "." ) > test <- readF(massvectorlist(info(mvl)),".") > test [1] Experiment : (020529r_dt_Pirellula) [1] Project : () [1] Nr (mv) : (100) > unlink(paste(info(test),".txt",sep="")) > > > > cleanEx(); ..nameEx <- "recalibrate.massvector" > > ### * recalibrate.massvector > > flush(stderr()); flush(stdout()) > > ### Name: recalibrate.massvector > ### Title: Precalibration > ### Aliases: recalibrate.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > mv2<-recalibrate(mv1) > plot(mv1[,1],mv1[,1]-mv2[,1],type="l") > > > > cleanEx(); ..nameEx <- "recalibrate.massvectorlist" > > ### * recalibrate.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: recalibrate.massvectorlist > ### Title: Precalibration > ### Aliases: recalibrate.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > mvl<-mvl[1:100] > pp <- recalibrate(mvl,PQM=8) > compare(pp[[1]],mvl[[1]],error=1,ppm=FALSE) > > > > cleanEx(); ..nameEx <- "residuals.massvector" > > ### * residuals.massvector > > flush(stderr()); flush(stdout()) > > ### Name: residuals.massvector > ### Title: Residues of 2 massvectors. > ### Aliases: residuals.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(mv2) > plot(resid(mv1,mv2,error=250,uniq=TRUE)) > > > > cleanEx(); ..nameEx <- "setParmsAssing.mylistobj" > > ### * setParmsAssing.mylistobj > > flush(stderr()); flush(stdout()) > > ### Name: setParms<-.mylistobj > ### Title: Field Access > ### Aliases: setParms<-.mylistobj > ### Keywords: misc > > ### ** Examples > > data(mv1) > res<-getrecalib(mv1) > setParms(res) <- list(info="test") > res class : calibrestat calibstat mylistobj info : test lengthmv : 49 Coeff.Intercept : 0.05744198 Coeff.Slope : 44.97976 PQM : 11.22155 tcoor : 1 1 > > > > cleanEx(); ..nameEx <- "setParmsAssing.myobj" > > ### * setParmsAssing.myobj > > flush(stderr()); flush(stdout()) > > ### Name: setParms<-.myobj > ### Title: Field Access > ### Aliases: setParms<-.myobj > ### Keywords: misc > > ### ** Examples > > data(mv1) > mv1 [1] info : (0_A1_1SRef) [1] coor : A=1 ; 1=1 mass area 1 842.4257 650.66 2 987.3931 180.30 3 1098.4314 3543.85 4 1112.4456 251.17 5 1129.4501 345.22 6 1147.4617 2261.36 7 1207.5648 1948.22 8 1257.5929 204.77 9 1296.6086 1528.91 10 1466.5645 257.75 11 1554.6257 600.61 12 1672.7671 5067.09 13 1686.7343 863.64 14 1694.6771 4959.24 15 1712.7915 619.39 16 1734.7188 665.85 17 1746.7566 574.26 18 1750.6805 7579.83 19 1754.6996 2695.35 20 1766.7008 402.83 21 1793.7116 1784.45 22 1807.6837 604.98 23 1810.7358 4088.75 24 1973.8298 1174.58 25 2002.8374 504.87 26 2090.8222 15183.35 27 2104.8344 1877.67 28 2128.7796 467.04 29 2189.8599 594.90 30 2210.8834 4582.26 31 2224.9057 1765.44 32 2232.9109 931.45 33 2238.9288 491.35 34 2245.9799 1913.02 35 2248.8393 727.08 36 2298.9676 2394.62 37 2312.9932 401.28 38 2465.0143 2196.50 39 2505.0601 360.43 40 2703.1986 1013.07 41 2811.1438 778.49 42 2914.3276 458.57 43 3000.3723 8538.46 44 3014.3788 1666.68 45 3057.3808 395.89 46 3120.2176 273.91 47 3331.4928 538.24 48 3346.5022 2513.62 49 3354.5540 415.73 > setParms(mv1) <- list(info="test") > mv1 [1] info : (test) [1] coor : A=1 ; 1=1 mass area 1 842.4257 650.66 2 987.3931 180.30 3 1098.4314 3543.85 4 1112.4456 251.17 5 1129.4501 345.22 6 1147.4617 2261.36 7 1207.5648 1948.22 8 1257.5929 204.77 9 1296.6086 1528.91 10 1466.5645 257.75 11 1554.6257 600.61 12 1672.7671 5067.09 13 1686.7343 863.64 14 1694.6771 4959.24 15 1712.7915 619.39 16 1734.7188 665.85 17 1746.7566 574.26 18 1750.6805 7579.83 19 1754.6996 2695.35 20 1766.7008 402.83 21 1793.7116 1784.45 22 1807.6837 604.98 23 1810.7358 4088.75 24 1973.8298 1174.58 25 2002.8374 504.87 26 2090.8222 15183.35 27 2104.8344 1877.67 28 2128.7796 467.04 29 2189.8599 594.90 30 2210.8834 4582.26 31 2224.9057 1765.44 32 2232.9109 931.45 33 2238.9288 491.35 34 2245.9799 1913.02 35 2248.8393 727.08 36 2298.9676 2394.62 37 2312.9932 401.28 38 2465.0143 2196.50 39 2505.0601 360.43 40 2703.1986 1013.07 41 2811.1438 778.49 42 2914.3276 458.57 43 3000.3723 8538.46 44 3014.3788 1666.68 45 3057.3808 395.89 46 3120.2176 273.91 47 3331.4928 538.24 48 3346.5022 2513.62 49 3354.5540 415.73 > > > > cleanEx(); ..nameEx <- "subset.mlist" > > ### * subset.mlist > > flush(stderr()); flush(stdout()) > > ### Name: subset.mlist > ### Title: Subset mlist > ### Aliases: subset.mlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > mvl<-subset(mvl,lengthmv>30) > > > > cleanEx(); ..nameEx <- "summary.calibintstat" > > ### * summary.calibintstat > > flush(stderr()); flush(stdout()) > > ### Name: summary.calibintstat > ### Title: Calibintstat Summaries > ### Aliases: summary.calibintstat > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(cal) > res<-getintcalib(mv1,cal,error=500,ppm=TRUE) > summary(res) info lengthmv Coef.Intercept Coef.Slope 0_A1_1SRef 49 98.1717377349405 -65.9617957111844 nrmatch Xcoor Ycoor R.Squared 9 1 1 0.094091401906758 Adjusted.R.squared p.value -0.0353241121065624 0.422054176762001 > > > > cleanEx(); ..nameEx <- "summary.calibspline" > > ### * summary.calibspline > > flush(stderr()); flush(stdout()) > > ### Name: summary.calibspline > ### Title: Calibspline Summaries > ### Aliases: summary.calibspline > ### Keywords: misc > > ### ** Examples > > data(ppg) > tmp <- getextcalib(ppg,error=200) Loading required package: modreg Warning: package 'modreg' has been merged into 'stats' > summary(tmp) Length Class Mode x 57 -none- numeric y 57 -none- numeric w 57 -none- numeric yin 57 -none- numeric lev 57 -none- numeric cv.crit 1 -none- numeric pen.crit 1 -none- numeric crit 1 -none- numeric df 1 -none- numeric spar 1 -none- numeric lambda 1 -none- numeric iparms 3 -none- numeric fit 5 smooth.spline.fit list call 3 -none- call allow 3 -none- character info 1 -none- character error 681 -none- numeric theo 681 -none- numeric > > > > cleanEx(); ..nameEx <- "summary.calibstat" > > ### * summary.calibstat > > flush(stderr()); flush(stdout()) > > ### Name: summary.calibstat > ### Title: Calibstat summary > ### Aliases: summary.calibstat > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(cal) > test<-getintcalib(mv1,cal) > summary(test) info lengthmv Coef.Intercept Coef.Slope 0_A1_1SRef 49 98.1717377349405 -65.9617957111844 nrmatch Xcoor Ycoor R.Squared 9 1 1 0.094091401906758 Adjusted.R.squared p.value -0.0353241121065624 0.422054176762001 > > > > cleanEx(); ..nameEx <- "summary.mlist" > > ### * summary.mlist > > flush(stderr()); flush(stdout()) > > ### Name: summary.mlist > ### Title: mist Summaries > ### Aliases: summary.mlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > summary(mvl) $info [1] "020529r_dt_Pirellula" $summary lengthmv mass.Min. mass.1st.Qu. mass.Median Min. : 8.00 Min. : 750.3 Min. : 750.3 Min. : 750.3 1st Qu.:25.00 1st Qu.: 758.4 1st Qu.: 758.4 1st Qu.: 758.4 Median :33.50 Median : 758.4 Median : 758.4 Median : 758.4 Mean :37.03 Mean : 804.5 Mean : 804.5 Mean : 804.5 3rd Qu.:49.25 3rd Qu.: 842.4 3rd Qu.: 842.4 3rd Qu.: 842.4 Max. :81.00 Max. :1296.0 Max. :1296.0 Max. :1296.0 mass.Mean mass.3rd.Qu. mass.Max. area.Min. Min. : 750.3 Min. : 750.3 Min. : 750.3 Min. : 74.43 1st Qu.: 758.4 1st Qu.: 758.4 1st Qu.: 758.4 1st Qu.: 152.75 Median : 758.4 Median : 758.4 Median : 758.4 Median : 212.60 Mean : 804.5 Mean : 804.5 Mean : 804.5 Mean : 335.21 3rd Qu.: 842.4 3rd Qu.: 842.4 3rd Qu.: 842.4 3rd Qu.: 301.18 Max. :1296.0 Max. :1296.0 Max. :1296.0 Max. :2780.00 area.1st.Qu. area.Median area.Mean area.3rd.Qu. Min. : 74.43 Min. : 74.43 Min. : 74.43 Min. : 74.43 1st Qu.: 152.75 1st Qu.: 152.75 1st Qu.: 152.75 1st Qu.: 152.75 Median : 212.60 Median : 212.60 Median : 212.60 Median : 212.60 Mean : 335.21 Mean : 335.21 Mean : 335.21 Mean : 335.21 3rd Qu.: 301.18 3rd Qu.: 301.18 3rd Qu.: 301.18 3rd Qu.: 301.18 Max. :2780.00 Max. :2780.00 Max. :2780.00 Max. :2780.00 area.Max. Min. : 74.43 1st Qu.: 152.75 Median : 212.60 Mean : 335.21 3rd Qu.: 301.18 Max. :2780.00 > data(mvl) > mvl<-mvl[1:100] > data(cal) > test <- getintcalib(mvl,cal,error=500) > summary(test) $info [1] "020529r_dt_Pirellula" $summary lengthmv Coef.Intercept Coef.Slope nrmatch Min. : 8.00 Min. :-82.5571 Min. :-1482.0484 Min. : 0.00 1st Qu.:25.00 1st Qu.: -0.6392 1st Qu.: -0.4781 1st Qu.: 7.00 Median :33.50 Median : 42.3227 Median : 83.7614 Median : 8.00 Mean :37.03 Mean : 65.6422 Mean : 13.0337 Mean : 8.19 3rd Qu.:49.25 3rd Qu.:119.0367 3rd Qu.: 150.5762 3rd Qu.: 9.25 Max. :81.00 Max. :353.8195 Max. : 444.1224 Max. :13.00 Xcoor Ycoor R.Squared Adjusted.R.squared Min. :1.00 Min. : 1.00 Min. :1.133e-06 Min. :-0.49962 1st Qu.:2.00 1st Qu.: 6.00 1st Qu.:5.014e-02 1st Qu.:-0.10353 Median :3.00 Median :12.00 Median :1.679e-01 Median : 0.04474 Mean :2.84 Mean :12.06 Mean :2.242e-01 Mean : 0.07809 3rd Qu.:4.00 3rd Qu.:18.00 3rd Qu.:3.539e-01 3rd Qu.: 0.23253 Max. :5.00 Max. :24.00 Max. :1.000e+00 Max. : 0.72068 NA's :1.000e+00 NA's : 2.00000 p.value Min. :0.008633 1st Qu.:0.143788 Median :0.290825 Mean :0.379478 3rd Qu.:0.599038 Max. :0.998004 NA's :2.000000 > > > > cleanEx(); ..nameEx <- "unlist.massvectorlist" > > ### * unlist.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: unlist.massvectorlist > ### Title: Flatten massvectorlist > ### Aliases: unlist.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > amv <- unlist(mvl) > length(amv) [1] 3703 > > > > cleanEx(); ..nameEx <- "writeF.massvector" > > ### * writeF.massvector > > flush(stderr()); flush(stdout()) > > ### Name: writeF.massvector > ### Title: Write massvector > ### Aliases: writeF.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > writeF(mv1,".") # writes the file in the home directory. > readF(massvector(info(mv1)),".") [1] info : (0_A1_1SRef) [1] coor : 1 ; 1 mass C2 1 842.4257 650.66 2 987.3931 180.30 3 1098.4314 3543.85 4 1112.4456 251.17 5 1129.4501 345.22 6 1147.4617 2261.36 7 1207.5648 1948.22 8 1257.5929 204.77 9 1296.6086 1528.91 10 1466.5645 257.75 11 1554.6257 600.61 12 1672.7671 5067.09 13 1686.7343 863.64 14 1694.6771 4959.24 15 1712.7915 619.39 16 1734.7188 665.85 17 1746.7566 574.26 18 1750.6805 7579.83 19 1754.6996 2695.35 20 1766.7008 402.83 21 1793.7116 1784.45 22 1807.6837 604.98 23 1810.7358 4088.75 24 1973.8298 1174.58 25 2002.8374 504.87 26 2090.8222 15183.35 27 2104.8344 1877.67 28 2128.7796 467.04 29 2189.8599 594.90 30 2210.8834 4582.26 31 2224.9057 1765.44 32 2232.9109 931.45 33 2238.9288 491.35 34 2245.9799 1913.02 35 2248.8393 727.08 36 2298.9676 2394.62 37 2312.9932 401.28 38 2465.0143 2196.50 39 2505.0601 360.43 40 2703.1986 1013.07 41 2811.1438 778.49 42 2914.3276 458.57 43 3000.3723 8538.46 44 3014.3788 1666.68 45 3057.3808 395.89 46 3120.2176 273.91 47 3331.4928 538.24 48 3346.5022 2513.62 49 3354.5540 415.73 > file.remove(paste(info(mv1),".txt",sep="")) [1] TRUE > > > > cleanEx(); ..nameEx <- "wsFilter.massvector" > > ### * wsFilter.massvector > > flush(stderr()); flush(stdout()) > > ### Name: wsFilter.massvector > ### Title: Smilanski Filtering > ### Aliases: wsFilter.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > tmp <- wsFilter(mv1,peptide=FALSE) > plot(tmp) [1] "x has length 0!" > tmp <- wsFilter(mv1,peptide=TRUE) > plot(tmp) > > > > cleanEx(); ..nameEx <- "wsFilter.massvectorlist" > > ### * wsFilter.massvectorlist > > flush(stderr()); flush(stdout()) > > ### Name: wsFilter.massvectorlist > ### Title: Smilanski Filtering > ### Aliases: wsFilter.massvectorlist > ### Keywords: misc > > ### ** Examples > > data(mvl) > res <- wsFilter(mvl,peptides = TRUE) > plot(res) > res2 <- wsFilter(mvl,peptides = FALSE) > plot(res2,col=2,add=TRUE) > image(res2,what="lengthmv") > hist(res) > hist(res2,col=2,add=TRUE) > > > > cleanEx(); ..nameEx <- "wsdist.massvector" > > ### * wsdist.massvector > > flush(stderr()); flush(stdout()) > > ### Name: wsdist.massvector > ### Title: Wool Smilanski Distance Matrix > ### Aliases: wsdist.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > plot(hclust(wsdist(mv1),method="single")) > > > > cleanEx(); ..nameEx <- "wsiFilter.massvector" > > ### * wsiFilter.massvector > > flush(stderr()); flush(stdout()) > > ### Name: wsiFilter.massvector > ### Title: Smilanski Filtering > ### Aliases: wsiFilter.massvector > ### Keywords: misc > > ### ** Examples > > data(mv1) > data(mv2) > length(mv1) [1] 49 > length(wsFilter(mv1)) [1] 49 > length(mv2) [1] 25 > length(wsFilter(mv2)) [1] 25 > > > > ### *