Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-18 17:58 -0400 (Tue, 18 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4758 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4492 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 2083/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
STATegRa 1.40.0 (landing page) David Gomez-Cabrero
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the STATegRa package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/STATegRa.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: STATegRa |
Version: 1.40.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:STATegRa.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings STATegRa_1.40.0.tar.gz |
StartedAt: 2024-06-17 04:23:08 -0400 (Mon, 17 Jun 2024) |
EndedAt: 2024-06-17 04:27:52 -0400 (Mon, 17 Jun 2024) |
EllapsedTime: 284.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: STATegRa.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:STATegRa.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings STATegRa_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/STATegRa.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘STATegRa/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘STATegRa’ version ‘1.40.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘STATegRa’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE modelSelection,list-numeric-character: no visible binding for global variable ‘components’ modelSelection,list-numeric-character: no visible binding for global variable ‘mylabel’ plotVAF,caClass: no visible binding for global variable ‘comp’ plotVAF,caClass: no visible binding for global variable ‘VAF’ plotVAF,caClass: no visible binding for global variable ‘block’ selectCommonComps,list-numeric: no visible binding for global variable ‘comps’ selectCommonComps,list-numeric: no visible binding for global variable ‘block’ selectCommonComps,list-numeric: no visible binding for global variable ‘comp’ selectCommonComps,list-numeric: no visible binding for global variable ‘ratio’ Undefined global functions or variables: VAF block comp components comps mylabel ratio * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘STATEgRa_Example.omicsCLUST.R’ Running ‘STATEgRa_Example.omicsPCA.R’ Running ‘STATegRa_Example.omicsNPC.R’ Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/STATegRa.Rcheck/00check.log’ for details.
STATegRa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL STATegRa ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘STATegRa’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (STATegRa)
STATegRa.Rcheck/tests/runTests.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("STATegRa") Common components [1] 2 Distinctive components [[1]] [1] 0 [[2]] [1] 0 Common components [1] 2 Distinctive components [[1]] [1] 1 [[2]] [1] 1 Common components [1] 2 Distinctive components [[1]] [1] 2 [[2]] [1] 2 RUNIT TEST PROTOCOL -- Mon Jun 17 04:25:57 2024 *********************************************** Number of test functions: 4 Number of errors: 0 Number of failures: 0 1 Test Suite : STATegRa RUnit Tests - 4 test functions, 0 errors, 0 failures Number of test functions: 4 Number of errors: 0 Number of failures: 0 Warning messages: 1: In rownames(pData) == colnames(exprs) : longer object length is not a multiple of shorter object length 2: In modelSelection(Input = list(B1, B2), Rmax = 4, fac.sel = "%accum", : Rmax cannot be higher than the minimum of components selected for each block. Rmax fixed to: 2 3: In modelSelection(Input = list(B1, B2), Rmax = 4, fac.sel = "fixed.num", : Rmax cannot be higher than the minimum of components selected for each block. Rmax fixed to: 3 > > proc.time() user system elapsed 3.056 0.193 3.238
STATegRa.Rcheck/tests/STATEgRa_Example.omicsCLUST.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > ########################################### > ########### EXAMPLE OF THE OMICSCLUSTERING > ########################################### > require(STATegRa) Loading required package: STATegRa > > ############################################# > ## PART 1: CREATING a bioMap CLASS > ############################################# > ####### This part creates or reads the map between features. > ####### In the present example the map is downloaded from a resource. > ####### then the class is created. > > #load("../data/STATegRa_S2.rda") > data(STATegRa_S2) > > MAP.SYMBOL<-bioMap(name = "Symbol-miRNA", + metadata = list(type_v1="Gene",type_v2="miRNA", + source_database="targetscan.Hs.eg.db", + data_extraction="July2014"), + map=mapdata) > > > ############################################# > ## PART 2: CREATING a bioDist CLASS > ############################################# > ##### In the second part given a set of main features and surrogate feautres, > ##### the profile of the main features is computed through the surrogate features. > > # Load Data > data(STATegRa_S1) > #load("../data/STATegRa.S1.Rdata") > > ## Create ExpressionSets > # source("../R/STATegRa_omicsPCA_classes_and_methods.R") > # Block1 - Expression data > mRNA.ds <- createOmicsExpressionSet(Data=Block1,pData=ed,pDataDescr=c("classname")) > # Block2 - miRNA expression data > miRNA.ds <- createOmicsExpressionSet(Data=Block2,pData=ed,pDataDescr=c("classname")) > > # Create Gene-gene distance computed through miRNA data > bioDistmiRNA<-bioDist(referenceFeatures = rownames(Block1), + reference = "Var1", + mapping = MAP.SYMBOL, + surrogateData = miRNA.ds, ### miRNA data + referenceData = mRNA.ds, ### mRNA data + maxitems=2, + selectionRule="sd", + expfac=NULL, + aggregation = "sum", + distance = "spearman", + noMappingDist = 0, + filtering = NULL, + name = "mRNAbymiRNA") > > require(Biobase) Loading required package: Biobase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' 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, aperm, 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, table, tapply, union, unique, unsplit, 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")'. > > # Create Gene-gene distance through mRNA data > bioDistmRNA<-bioDistclass(name = "mRNAbymRNA", + distance = cor(t(exprs(mRNA.ds)),method="spearman"), + map.name = "id", + map.metadata = list(), + params = list()) > > ############################################# > ## PART 3: CREATING a LISTOF WEIGTHED DISTANCES MATRICES: bioDistWList > ############################################# > > bioDistList<-list(bioDistmRNA,bioDistmiRNA) > weights<-matrix(0,4,2) > weights[,1]<-c(0,0.33,0.67,1) > weights[,2]<-c(1,0.67,0.33,0)# > > bioDistWList<-bioDistW(referenceFeatures = rownames(Block1), + bioDistList = bioDistList, + weights=weights) > length(bioDistWList) [1] 4 > > ############################################# > ## PART 4: DEFINING THE STRENGTH OF ASSOCIATIONS IN GENERAL > ############################################# > > bioDistWPlot(referenceFeatures = rownames(Block1) , + listDistW = bioDistWList, + method.cor="spearman") Warning messages: 1: In cor.test.default(getDist(listDistW[[i]])[referenceFeatures, referenceFeatures], : Cannot compute exact p-value with ties 2: In cor.test.default(getDist(listDistW[[i]])[referenceFeatures, referenceFeatures], : Cannot compute exact p-value with ties 3: In cor.test.default(getDist(listDistW[[i]])[referenceFeatures, referenceFeatures], : Cannot compute exact p-value with ties 4: In plot.window(...) : axis(2, *): range of values ( 0) is small wrt |M| = 3e-09 --> not pretty() 5: In plot.window(...) : axis(2, *): range of values ( 0) is small wrt |M| = 3e-09 --> not pretty() 6: In plot.window(...) : axis(2, *): range of values ( 0) is small wrt |M| = 3e-09 --> not pretty() 7: In plot.window(...) : axis(2, *): range of values ( 0) is small wrt |M| = 3e-09 --> not pretty() > > ############################################# > ## PART 5: DEFINING THE ASSOCIATIONS FOR A GIVEN GENE > ############################################# > > ## IDH1 > > IDH1.F<-bioDistFeature(Feature = "IDH1" , + listDistW = bioDistWList, + threshold.cor=0.7) > bioDistFeaturePlot(data=IDH1.F) > > ## PDGFRA > > #PDGFRA.F<-bioDistFeature(Feature = "PDGFRA" , > # listDistW = bioDistWList, > # threshold.cor=0.7) > #bioDistFeaturePlot(data=PDGFRA.F,name="../vignettes/PDGFRA.png") > > ## EGFR > #EGFR.F<-bioDistFeature(Feature = "EGFR" , > # listDistW = bioDistWList, > # threshold.cor=0.7) > #bioDistFeaturePlot(data=EGFR.F,name="../vignettes/EGFR.png") > > ## MGMT > #MGMT.F<-bioDistFeature(Feature = "MGMT" , > # listDistW = bioDistWList, > # threshold.cor=0.5) > #bioDistFeaturePlot(data=MGMT.F,name="../vignettes/MGMT.png") > > > > > > proc.time() user system elapsed 21.722 0.568 22.279
STATegRa.Rcheck/tests/STATegRa_Example.omicsNPC.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > rm(list = ls()) > require("STATegRa") Loading required package: STATegRa > # Load the data > data("TCGA_BRCA_Batch_93") > # Setting dataTypes > dataTypes <- c("count", "count", "continuous") > # Setting methods to combine pvalues > combMethods = c("Fisher", "Liptak", "Tippett") > # Setting number of permutations > numPerms = 1000 > # Setting number of cores > numCores = 1 > # Setting holistOmics to print out the steps that it performs. > verbose = TRUE > # Run holistOmics analysis. > output <- omicsNPC(dataInput = TCGA_BRCA_Data, dataTypes = dataTypes, combMethods = combMethods, numPerms = numPerms, numCores = numCores, verbose = verbose) Compute initial statistics on data Building NULL distributions by permuting data Compute pseudo p-values based on NULL distributions... NPC p-values calculation... > > proc.time() user system elapsed 58.431 0.441 58.862
STATegRa.Rcheck/tests/STATEgRa_Example.omicsPCA.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > ########################################### > ########### EXAMPLE OF THE OMICSPCA > ########################################### > require(STATegRa) Loading required package: STATegRa > > # g_legend (not exported by STATegRa any more) > ## code from https://github.com/hadley/ggplot2/wiki/Share-a-legend-between-two-ggplot2-graphs > g_legend<-function(a.gplot){ + tmp <- ggplot_gtable(ggplot_build(a.gplot)) + leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box") + legend <- tmp$grobs[[leg]] + return(legend)} > > ######################### > ## PART 1. Load data > > ## Load data > data(STATegRa_S3) > > ls() [1] "Block1.PCA" "Block2.PCA" "ed.PCA" "g_legend" > > ## Create ExpressionSets > # Block1 - Expression data > B1 <- createOmicsExpressionSet(Data=Block1.PCA,pData=ed.PCA,pDataDescr=c("classname")) > # Block2 - miRNA expression data > B2 <- createOmicsExpressionSet(Data=Block2.PCA,pData=ed.PCA,pDataDescr=c("classname")) > > ######################### > ## PART 2. Model Selection > > require(grid) Loading required package: grid > require(gridExtra) Loading required package: gridExtra > require(ggplot2) Loading required package: ggplot2 > > ## Select the optimal components > ms <- modelSelection(Input=list(B1,B2),Rmax=4,fac.sel="single%",varthreshold=0.03,center=TRUE,scale=TRUE,weight=TRUE) Common components [1] 2 Distinctive components [[1]] [1] 2 [[2]] [1] 2 > > > ######################### > ## PART 3. Component Analysis > > ## 3.1 Component analysis of the three methods > discoRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),method="DISCOSCA",Rcommon=2,Rspecific=c(2,2),center=TRUE, + scale=TRUE,weight=TRUE) > jiveRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),method="JIVE",Rcommon=2,Rspecific=c(2,2),center=TRUE, + scale=TRUE,weight=TRUE) > o2plsRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),method="O2PLS",Rcommon=2,Rspecific=c(2,2),center=TRUE, + scale=TRUE,weight=TRUE) > > ## 3.2 Exploring scores structures > > # Exploring DISCO-SCA scores structure > discoRes@scores$common ## Common scores 1 2 sample1 -0.0781574320 0.0431502408 sample2 0.1192218419 -0.0294088111 sample3 0.0531412091 0.0746839801 sample4 -0.0292975122 0.0005960404 sample5 -0.0202091734 -0.0110463762 sample6 -0.1226089059 -0.1053467247 sample7 -0.1078928137 0.0322475429 sample8 -0.1782895285 -0.1449363759 sample9 -0.0468698104 0.0455174269 sample10 0.0036030543 -0.0420110883 sample11 0.0035566481 0.0566292539 sample12 -0.1006128919 -0.0641380791 sample13 0.1174408355 -0.0907488219 sample14 -0.0981203270 -0.0617738273 sample15 -0.0085334325 0.0087013172 sample16 -0.0783148651 -0.1581294692 sample17 0.1483609915 -0.0638581887 sample18 0.0963086227 -0.0556640425 sample19 0.0217244097 0.0720086369 sample20 0.0635636387 0.0779652913 sample21 0.0201840375 -0.1566391358 sample22 -0.0218268772 0.0764104142 sample23 -0.0852041988 0.0032689210 sample24 0.1287170693 -0.1924542774 sample25 0.0430574163 0.0456566526 sample26 0.1453896845 -0.0541511752 sample27 0.0197488777 0.1185656430 sample28 0.1025336317 -0.0650685307 sample29 -0.0706018519 0.0682987850 sample30 0.1295627494 0.0066768767 sample31 -0.1147449133 -0.1232686847 sample32 0.0374310864 -0.0380178416 sample33 -0.0599516034 -0.0136867595 sample34 0.0984200808 -0.0375321315 sample35 0.0543098346 0.0378105565 sample36 -0.1403625469 0.0343755466 sample37 -0.0228941934 0.0732845406 sample38 0.0222077221 0.0962594715 sample39 0.0941738499 -0.0215199088 sample40 -0.0643801207 0.0687870153 sample41 0.0327638009 0.1232188142 sample42 0.0500431837 0.0292473560 sample43 0.0184498824 -0.0233011326 sample44 -0.1487898730 -0.1171353465 sample45 0.1050774206 -0.1123201214 sample46 0.1151195686 0.1094028608 sample47 0.0962593708 0.0288463524 sample48 -0.0004837284 0.0310278388 sample49 -0.1135207771 -0.1213972794 sample50 0.0123553117 0.1740743806 sample51 -0.0550529841 -0.1258886984 sample52 -0.0499121194 -0.0728544786 sample53 -0.1119773652 -0.1588014108 sample54 0.0360055683 -0.0228575696 sample55 -0.0210418976 -0.0006731890 sample56 0.0434169254 -0.0633126124 sample57 -0.0197824576 -0.1150713818 sample58 -0.0030439899 -0.0326098142 sample59 -0.0500253147 -0.0129419314 sample60 -0.0184278676 -0.0136085837 sample61 -0.0150299399 -0.0635026175 sample62 0.0304763856 0.0201318975 sample63 -0.1102252468 -0.1285976869 sample64 -0.1552588086 -0.0971168370 sample65 0.0058503073 -0.0207115443 sample66 0.0025605373 -0.0424319887 sample67 -0.1546634857 0.0661715952 sample68 -0.0536369303 0.0923683423 sample69 -0.0640330388 -0.0081983138 sample70 -0.0163517771 0.0663230126 sample71 0.0102537626 0.1345921522 sample72 0.0654196023 0.0196119229 sample73 0.1048556128 -0.0220938472 sample74 -0.0123799467 -0.0586115330 sample75 -0.0392077934 0.0209754905 sample76 -0.0648953400 0.0524764404 sample77 -0.1172922144 0.0201186759 sample78 0.1463068094 -0.0708472127 sample79 -0.0265211176 0.1603308274 sample80 -0.0279737145 0.0214204927 sample81 -0.0079211493 0.0738450967 sample82 0.1544236477 0.0361467947 sample83 0.0494211370 0.0050048203 sample84 0.0259038497 0.0346549598 sample85 -0.1116484380 0.0031497510 sample86 0.1306483002 0.0377215100 sample87 0.0554778201 0.0459748878 sample88 0.0301623853 -0.0382197612 sample89 0.1016866715 -0.0694033942 sample90 -0.0086819888 0.0201320128 sample91 -0.1578625359 0.2097828064 sample92 -0.0170936821 0.1655807222 sample93 0.0979806811 0.0121512256 sample94 -0.0131484104 0.0114932108 sample95 -0.0315682625 0.0758859217 sample96 -0.0024125609 0.0470135632 sample97 -0.0634545407 -0.0270331865 sample98 0.0359374634 0.0135488414 sample99 0.1009163328 -0.1124779902 sample100 -0.0551753146 -0.0246489528 sample101 0.0080118885 0.1627368637 sample102 0.0046444344 -0.0095631825 sample103 0.0472523175 0.0940393290 sample104 -0.0198159468 0.0591091604 sample105 0.0400237815 0.0160911947 sample106 0.0923808416 -0.0369017696 sample107 0.1019373945 -0.0224954161 sample108 0.0877091653 0.0128834225 sample109 -0.0864824375 0.0900941842 sample110 0.1223115536 0.0096085747 sample111 -0.0257354610 0.0936169146 sample112 0.0765286603 -0.0270347587 sample113 -0.0258803219 -0.0377497262 sample114 -0.0021138920 0.0882014883 sample115 -0.0303460190 0.0723585741 sample116 -0.0780508435 0.0685066448 sample117 -0.0536898093 0.0911908388 sample118 -0.0666651164 0.0236231122 sample119 -0.1021871643 0.2324936921 sample120 -0.0750216559 -0.0243379104 sample121 0.0756936398 -0.0942950554 sample122 0.0259628106 -0.0731987250 sample123 0.1037846252 0.0369197202 sample124 -0.0611207922 -0.0421723633 sample125 0.0738472726 -0.0066950195 sample126 -0.0972916451 -0.0762639960 sample127 -0.0824697640 0.0096637343 sample128 0.1249407648 -0.0929312632 sample129 0.0734067507 0.0434362920 sample130 0.0003502002 0.0309852661 sample131 -0.0930182822 -0.0155937100 sample132 -0.0736222805 -0.0733029834 sample133 0.0498397991 0.0462437404 sample134 -0.1644873500 -0.0720005573 sample135 0.0752297196 -0.0003817734 sample136 -0.0227145779 0.0495506039 sample137 -0.0564717423 0.0288915775 sample138 -0.0255988104 0.0610856997 sample139 -0.0621217818 -0.0235807669 sample140 0.0604152538 0.0435593254 sample141 -0.0246743956 -0.0532648755 sample142 0.0409560346 -0.0316279926 sample143 0.0077355231 0.0476896232 sample144 -0.0173240812 0.0156777890 sample145 -0.0485474502 -0.1202770652 sample146 -0.0419645645 0.0811281332 sample147 0.0977308336 0.0274840069 sample148 -0.0368256167 -0.0803979752 sample149 0.0072865789 0.1532986005 sample150 -0.1020825297 -0.0624774605 sample151 -0.0305399050 0.0289278139 sample152 0.0533594794 0.0638309166 sample153 0.0891627651 -0.1799578263 sample154 0.0727557463 0.0834160931 sample155 0.0880668570 0.0220819548 sample156 0.0276561064 0.0326625266 sample157 0.1155032182 -0.0183616047 sample158 0.0281507534 0.0104938589 sample159 -0.0663235711 -0.0443837347 sample160 0.0302643910 -0.0404265566 sample161 -0.0114715559 0.0591025427 sample162 0.1337087115 -0.1398135406 sample163 -0.1330124484 -0.1688781225 sample164 0.0150336116 -0.0028416274 sample165 -0.0076520249 0.0164128290 sample166 -0.0367794372 -0.0630662041 sample167 -0.1111988868 -0.0030057844 sample168 0.0672981600 -0.0446279320 sample169 0.0413004970 -0.0224394269 > discoRes@scores$dist[[1]] ## Distinctive scores for Block 1 1 2 sample1 0.0420514733 0.0867863094 sample2 0.0820828590 -0.0410977992 sample3 -0.0155899818 -0.0195182399 sample4 0.1001337142 -0.0410786642 sample5 0.0153466038 -0.0253259678 sample6 -0.0340325800 -0.0408223182 sample7 -0.0722579775 0.0002332204 sample8 0.0457499996 -0.0370016165 sample9 0.0086249281 0.0820184896 sample10 0.0423598662 -0.0083923260 sample11 -0.0022548633 0.0787766029 sample12 -0.0322105840 0.1479824691 sample13 0.0293889779 -0.0306748580 sample14 -0.0337482661 -0.0367506854 sample15 -0.0815539153 0.1275622455 sample16 -0.0508452187 0.0540604675 sample17 -0.0062596721 0.0041023729 sample18 -0.0705639833 -0.0351047704 sample19 0.0476841741 -0.0509598092 sample20 -0.0522962850 0.0715521824 sample21 0.0119126734 -0.0376093051 sample22 -0.0724393123 -0.0095625161 sample23 0.0992532175 0.0134288826 sample24 0.1595118057 0.0728662132 sample25 0.0920693395 -0.0749757245 sample26 0.0595540040 0.0848966079 sample27 -0.0826485648 -0.0086735486 sample28 0.0384788147 0.0440966907 sample29 -0.0777671589 0.1735308473 sample30 -0.1229471276 -0.0819005570 sample31 -0.0579846385 -0.0238644745 sample32 -0.0970393149 -0.0111426329 sample33 -0.1017588001 -0.0630442602 sample34 -0.0637922882 0.0377941694 sample35 -0.0789984475 -0.0229723251 sample36 -0.1224939265 -0.1274954983 sample37 -0.1798820744 -0.1673427500 sample38 -0.0466304514 0.0888160907 sample39 0.0168687634 0.0421533763 sample40 -0.1756392068 -0.1526642425 sample41 -0.0042370742 0.0004928770 sample42 0.0447849735 -0.0651505000 sample43 -0.0482308396 -0.0253529289 sample44 0.1986714724 -0.0545777767 sample45 0.0741836394 0.0054703332 sample46 -0.0478772098 -0.0007072059 sample47 -0.0608188535 0.0481622611 sample48 0.1381489432 0.0578287812 sample49 0.0530520379 -0.1405532785 sample50 0.0173799900 0.1602389632 sample51 -0.0462561088 0.0303473849 sample52 -0.0280065067 0.0280388402 sample53 -0.0667621529 0.0237702057 sample54 -0.0121833547 -0.0521354324 sample55 -0.0182395886 0.0221328424 sample56 0.0001255525 0.0030907371 sample57 -0.0316675559 0.0530190298 sample58 -0.0393918188 -0.0297798751 sample59 -0.1278290919 -0.0546527988 sample60 -0.1486985178 0.1069156522 sample61 -0.0793122552 0.0569796513 sample62 -0.1172801014 -0.0149198529 sample63 0.0028726615 0.1300519865 sample64 -0.0237364810 0.1073287737 sample65 0.0126534902 0.0589808442 sample66 0.0468194791 -0.0771072674 sample67 -0.1494264536 -0.0769860345 sample68 -0.0977961089 -0.0577351102 sample69 -0.0403087308 0.0156042106 sample70 -0.0221531206 0.0315440935 sample71 0.0546434760 -0.0272396451 sample72 -0.1107487752 -0.0537319417 sample73 -0.0906761274 0.0579966579 sample74 -0.0586555431 0.0121421663 sample75 -0.0390493225 0.0349282793 sample76 0.0022960795 -0.1676558800 sample77 0.0232096273 -0.2067302789 sample78 0.0929754831 -0.0434939440 sample79 0.1619497010 -0.0378114216 sample80 -0.0680365496 0.1424663465 sample81 0.0530784183 -0.0358350847 sample82 -0.0266821936 -0.0577445120 sample83 -0.1517235165 -0.0448554392 sample84 0.0570967205 -0.0273813235 sample85 -0.1086289698 -0.1228119361 sample86 -0.0833859899 -0.0442915019 sample87 -0.0022018320 -0.0943906866 sample88 0.0078224858 -0.1140506519 sample89 -0.0611057337 -0.0094585161 sample90 -0.0022928048 -0.0936253998 sample91 -0.0433590299 0.3205982735 sample92 0.1815335738 -0.0334680261 sample93 -0.0267630748 0.0614429013 sample94 -0.0181877753 0.0605090398 sample95 0.0720375833 -0.0013045645 sample96 0.0559714873 -0.0118791409 sample97 0.0217411004 0.0195414156 sample98 -0.0379177372 0.0588357088 sample99 0.0792427117 -0.0151273750 sample100 -0.0222116477 -0.0023321432 sample101 0.0387228818 0.1224226198 sample102 0.2094614182 -0.0516442545 sample103 -0.0138481076 0.0301051928 sample104 0.0807987121 -0.0162718902 sample105 0.0520493426 -0.1229665154 sample106 0.0192613231 -0.0185238171 sample107 -0.0319017183 0.0405123278 sample108 0.0140691014 0.0163421382 sample109 0.1831930228 0.0613007611 sample110 0.0292790604 -0.0199849074 sample111 0.1423252198 0.0327340358 sample112 -0.0426332888 -0.0029083452 sample113 0.0771904496 0.0268733681 sample114 0.0241641585 -0.0184080427 sample115 0.1959015687 0.0460130738 sample116 0.1394476056 -0.0530805762 sample117 0.1672361962 -0.1386536357 sample118 0.0448344282 -0.0117621916 sample119 0.0910386629 0.2217433375 sample120 0.0331392185 -0.0057274477 sample121 -0.0307575049 0.1392506553 sample122 0.0839781094 -0.0291994378 sample123 -0.0239650346 -0.0642163744 sample124 0.0909150567 0.0130419545 sample125 0.0065350893 -0.1092631815 sample126 -0.0935311972 0.1368284030 sample127 -0.0035387885 0.0292755634 sample128 0.0660295323 0.1018566369 sample129 -0.0693638514 -0.0695421777 sample130 -0.0008493373 -0.0669704336 sample131 -0.0431024050 0.0174064858 sample132 0.0637040034 0.0029374762 sample133 0.0289494867 -0.0390818833 sample134 -0.0446203156 0.0456334511 sample135 -0.0712336985 0.0521634926 sample136 -0.0596270916 0.0197299288 sample137 -0.0793151919 -0.0380628342 sample138 0.0973548442 -0.0454218237 sample139 -0.0539904758 -0.1534327375 sample140 -0.0850826946 0.0955814486 sample141 0.0192681784 -0.0554450052 sample142 0.0672261988 -0.0461320883 sample143 0.0303730511 -0.0519260237 sample144 0.0089364630 0.0145814912 sample145 0.0638769761 0.0122258464 sample146 -0.0585856199 0.0063083310 sample147 -0.0894133289 -0.1124615744 sample148 0.0216366871 -0.0615967101 sample149 0.0515420929 -0.0839903504 sample150 -0.0568283448 -0.0124468927 sample151 0.0789532460 -0.0261831161 sample152 0.0330753533 0.1306443587 sample153 0.1751930922 0.1497732221 sample154 -0.0421424220 -0.0037010230 sample155 -0.0680177445 0.0095711193 sample156 -0.0388911077 0.1057562932 sample157 -0.0314769453 0.0561367414 sample158 -0.0329620510 0.0353947305 sample159 0.0398416516 -0.1007373745 sample160 -0.0424938769 0.0108496164 sample161 0.0888371412 -0.0679700147 sample162 0.0027475664 0.1237843897 sample163 0.0126104983 0.0725434393 sample164 0.0566779702 -0.0458324161 sample165 0.0315336456 -0.0236362343 sample166 0.0612058048 -0.0425232997 sample167 -0.0142729876 0.0179308272 sample168 0.0169503438 -0.0769617882 sample169 -0.0675080384 0.0131505307 > discoRes@scores$dist[[2]] ## Distinctive scores for Block 2 1 2 sample1 -0.0012329704 -1.635717e-01 sample2 -0.0724350166 -6.021264e-03 sample3 -0.0188460431 -1.080036e-01 sample4 0.0390145234 3.114047e-04 sample5 0.1774811606 -2.996385e-02 sample6 -0.0451444503 -3.455858e-02 sample7 -0.0226466164 -7.020152e-03 sample8 -0.1033680373 -9.856790e-03 sample9 0.1350011836 8.979098e-02 sample10 0.1259887158 -5.097854e-02 sample11 0.0979788462 7.086534e-02 sample12 -0.0863019170 -8.620317e-02 sample13 -0.1381401142 1.828007e-01 sample14 -0.0615073899 -2.642803e-02 sample15 0.0381598991 -3.101663e-02 sample16 -0.0048776839 1.271834e-03 sample17 -0.0788481044 -1.547554e-02 sample18 -0.0884188811 -3.795486e-02 sample19 0.0703044401 -1.084004e-01 sample20 -0.0025585390 7.975875e-02 sample21 0.0941601478 -4.126742e-02 sample22 -0.0550273341 -7.806742e-02 sample23 0.0679495252 -4.102006e-02 sample24 -0.1310962997 1.649309e-01 sample25 0.0113585241 -4.426863e-02 sample26 -0.1402946014 2.016543e-02 sample27 0.0261561280 1.588456e-03 sample28 -0.0724198787 5.850592e-02 sample29 -0.0330058448 2.060837e-03 sample30 -0.0228752525 -2.015429e-02 sample31 -0.0635068046 -6.670334e-02 sample32 0.0685099631 -4.955273e-02 sample33 -0.0777765235 -1.272078e-01 sample34 0.0157842377 -3.024314e-02 sample35 -0.0529632616 1.500972e-01 sample36 0.0070900986 2.025307e-01 sample37 -0.0442420339 1.802089e-01 sample38 -0.0781511206 -3.676419e-02 sample39 0.0120331794 -3.388842e-02 sample40 -0.0473291829 1.471562e-01 sample41 0.0228189508 -2.673554e-02 sample42 -0.0245360293 -7.960867e-02 sample43 0.1036362763 -8.229577e-02 sample44 -0.1012228948 7.049450e-02 sample45 0.0013731865 -2.450912e-02 sample46 -0.0558509910 2.947395e-03 sample47 -0.0380481114 4.554174e-02 sample48 0.0784342069 4.888979e-02 sample49 -0.0605164092 -1.162356e-02 sample50 0.0530079409 -2.737932e-02 sample51 0.1514646476 5.678344e-02 sample52 0.1860935255 1.246717e-01 sample53 -0.0064177203 -2.700994e-02 sample54 0.0697038308 -2.308389e-02 sample55 0.1633577053 1.366441e-02 sample56 0.1011485058 4.682204e-02 sample57 0.1730374209 1.609603e-01 sample58 -0.0071384726 -1.666955e-02 sample59 -0.0030461607 3.005286e-02 sample60 0.0215835344 2.665878e-01 sample61 0.1510583675 1.002385e-01 sample62 -0.0925533904 -4.845840e-02 sample63 -0.0596311911 -4.137023e-02 sample64 -0.0449225848 -2.600582e-03 sample65 0.0939383712 -4.406910e-02 sample66 0.1063400658 -5.709994e-02 sample67 -0.0201589727 2.361728e-01 sample68 0.0037203361 2.418390e-02 sample69 -0.0645161241 -1.155622e-01 sample70 -0.1013440007 -1.351789e-01 sample71 -0.0016467798 -2.976841e-02 sample72 0.0328893068 -2.835857e-02 sample73 0.0275080026 -5.148186e-02 sample74 0.1341719624 -7.895281e-02 sample75 0.0951575690 -3.943184e-02 sample76 -0.0864721892 3.034992e-02 sample77 -0.1035749555 -2.545353e-02 sample78 -0.1575644251 4.939594e-02 sample79 0.0189137173 4.874679e-02 sample80 0.1384140649 4.265131e-05 sample81 -0.0118846449 -6.357931e-02 sample82 -0.1675308135 3.533913e-02 sample83 -0.0065673376 -7.812609e-02 sample84 0.1486891594 -3.109058e-02 sample85 -0.0532724306 7.417885e-02 sample86 -0.1138477285 -1.914189e-05 sample87 0.0432864046 6.080473e-02 sample88 0.0433450393 1.402491e-01 sample89 0.0331205720 -1.395401e-02 sample90 -0.0607412839 -8.610414e-02 sample91 -0.0566272321 1.303747e-01 sample92 -0.0359582388 1.061604e-01 sample93 -0.0433646377 -4.443634e-02 sample94 -0.0477291331 -1.059574e-01 sample95 -0.0249595753 -3.980525e-02 sample96 0.0035218977 -9.293928e-02 sample97 -0.0066048855 -1.527231e-01 sample98 0.0020366814 -5.579550e-02 sample99 -0.0886616272 -3.728226e-02 sample100 -0.1091259155 -3.560419e-02 sample101 -0.0739726376 -4.317998e-02 sample102 0.0574461025 -2.783915e-02 sample103 0.0142731111 9.705563e-03 sample104 0.0710395248 4.068350e-02 sample105 0.0980831311 -3.452953e-02 sample106 -0.0254259354 3.628984e-02 sample107 -0.0160653516 -9.173394e-02 sample108 -0.0200987679 -2.379692e-02 sample109 -0.0389780639 1.692358e-02 sample110 -0.0326304859 2.988109e-02 sample111 0.0676937553 -6.038213e-02 sample112 0.0167883419 5.336938e-03 sample113 0.0969216936 -2.757605e-02 sample114 -0.0026398331 -9.209156e-02 sample115 -0.0308047336 1.603822e-02 sample116 -0.1240307106 1.273000e-01 sample117 0.0334729115 5.392710e-02 sample118 -0.1037152876 6.252431e-02 sample119 -0.1064176410 1.196202e-01 sample120 -0.0771355167 -1.004933e-01 sample121 -0.0129350817 3.181975e-02 sample122 0.0847492150 -5.568328e-02 sample123 -0.0041336748 7.693183e-03 sample124 -0.0583458115 -8.396390e-02 sample125 0.0634844550 -5.232540e-02 sample126 -0.0662581006 -1.091732e-01 sample127 -0.0865024635 -1.094176e-01 sample128 -0.0627817578 -1.470964e-02 sample129 -0.0336276411 -4.007858e-02 sample130 -0.0293517761 -8.046117e-02 sample131 -0.0469197643 -2.209746e-03 sample132 -0.0241740826 -1.248598e-01 sample133 0.0907303237 1.466700e-02 sample134 -0.0350842055 7.539662e-02 sample135 0.0001333433 9.185382e-03 sample136 -0.0335876031 -9.860273e-02 sample137 -0.0640148873 -7.554469e-02 sample138 0.0060964846 -1.742762e-02 sample139 -0.0592084419 5.614969e-02 sample140 0.0427985993 -1.099550e-02 sample141 0.0618796284 -9.301038e-02 sample142 0.0898554417 3.573416e-02 sample143 0.0817389285 8.880524e-02 sample144 0.0787754776 -3.821392e-02 sample145 0.1085821529 1.569476e-01 sample146 -0.0589557854 -4.373359e-02 sample147 -0.0495330389 7.277210e-03 sample148 0.1161592719 9.079072e-03 sample149 -0.0121579308 7.788375e-02 sample150 -0.0314512533 3.520213e-02 sample151 0.0575382155 -1.945353e-02 sample152 -0.0494542030 7.025538e-02 sample153 -0.0941332892 2.153297e-01 sample154 -0.0335931916 2.078729e-02 sample155 0.0690457673 -2.780410e-02 sample156 0.1039901634 -6.292525e-02 sample157 -0.0408645800 8.065517e-03 sample158 0.1018105332 7.816873e-03 sample159 -0.0281730593 -1.207206e-02 sample160 0.1643052990 2.978097e-03 sample161 0.0374329305 8.524610e-02 sample162 -0.0804535430 8.349754e-02 sample163 -0.0743228113 -1.406225e-02 sample164 0.1208805968 -2.139461e-02 sample165 0.1608115925 2.025191e-02 sample166 -0.0425944733 -2.660715e-02 sample167 -0.0226849479 -4.464281e-02 sample168 -0.0180735644 -7.466222e-04 sample169 0.0190779024 2.645402e-02 > # Exploring O2PLS scores structure > o2plsRes@scores$common[[1]] ## Common scores for Block 1 [,1] [,2] sample1 -0.0572060227 -1.729087e-02 sample2 0.0875245208 1.112588e-02 sample3 0.0403482602 -3.168994e-02 sample4 -0.0218345996 4.052760e-06 sample5 -0.0150905011 4.795041e-03 sample6 -0.0924362933 4.511003e-02 sample7 -0.0793066751 -1.243823e-02 sample8 -0.1342997187 6.215220e-02 sample9 -0.0338886944 -1.854401e-02 sample10 0.0020547173 1.749421e-02 sample11 0.0037275602 -2.364116e-02 sample12 -0.0753094533 2.772698e-02 sample13 0.0856160091 3.679963e-02 sample14 -0.0737457307 2.668452e-02 sample15 -0.0062111746 -3.554864e-03 sample16 -0.0602355268 6.675115e-02 sample17 0.1086768843 2.524534e-02 sample18 0.0702999472 2.231671e-02 sample19 0.0173785882 -3.024846e-02 sample20 0.0484173812 -3.310904e-02 sample21 0.0124657042 6.517144e-02 sample22 -0.0140989936 -3.159137e-02 sample23 -0.0627028403 -5.393710e-04 sample24 0.0919972100 7.909297e-02 sample25 0.0326998483 -1.945206e-02 sample26 0.1064741246 2.120849e-02 sample27 0.0166058995 -4.964993e-02 sample28 0.0743504770 2.614211e-02 sample29 -0.0511008491 -2.782647e-02 sample30 0.0962250842 -3.974893e-03 sample31 -0.0869563008 5.250819e-02 sample32 0.0271858919 1.552005e-02 sample33 -0.0448364581 6.243160e-03 sample34 0.0718415218 1.469396e-02 sample35 0.0403086451 -1.632629e-02 sample36 -0.1036402827 -1.304320e-02 sample37 -0.0159385744 -3.036525e-02 sample38 0.0182198369 -4.034805e-02 sample39 0.0690363619 8.058350e-03 sample40 -0.0467312750 -2.810325e-02 sample41 0.0263674438 -5.171216e-02 sample42 0.0374578960 -1.268634e-02 sample43 0.0132336869 9.536642e-03 sample44 -0.1119154428 5.028683e-02 sample45 0.0759639367 4.587903e-02 sample46 0.0871885519 -4.670385e-02 sample47 0.0721490571 -1.288540e-02 sample48 0.0005086144 -1.290565e-02 sample49 -0.0858177028 5.173760e-02 sample50 0.0118992665 -7.276215e-02 sample51 -0.0426446855 5.306205e-02 sample52 -0.0381605826 3.086785e-02 sample53 -0.0855757630 6.730043e-02 sample54 0.0261723092 9.184260e-03 sample55 -0.0156418304 4.682404e-04 sample56 0.0307831193 2.597550e-02 sample57 -0.0157242103 4.829381e-02 sample58 -0.0031174404 1.359898e-02 sample59 -0.0373001859 5.868397e-03 sample60 -0.0142609099 5.831654e-03 sample61 -0.0122255144 2.663579e-02 sample62 0.0228002942 -8.692265e-03 sample63 -0.0833127581 5.473229e-02 sample64 -0.1166548159 4.196500e-02 sample65 0.0038808902 8.568590e-03 sample66 0.0011561811 1.766612e-02 sample67 -0.1129311062 -2.608702e-02 sample68 -0.0382526429 -3.804045e-02 sample69 -0.0476502440 4.003241e-03 sample70 -0.0110329882 -2.752719e-02 sample71 0.0096850282 -5.627056e-02 sample72 0.0487124704 -8.800131e-03 sample73 0.0773058132 8.239864e-03 sample74 -0.0102488176 2.454957e-02 sample75 -0.0286613976 -8.387293e-03 sample76 -0.0472655595 -2.129315e-02 sample77 -0.0865043074 -7.296820e-03 sample78 0.1070293698 2.818346e-02 sample79 -0.0165060681 -6.659721e-02 sample80 -0.0206765949 -8.712112e-03 sample81 -0.0050943615 -3.079175e-02 sample82 0.1153622361 -1.647054e-02 sample83 0.0367979217 -2.538114e-03 sample84 0.0199463070 -1.468961e-02 sample85 -0.0827122185 -2.709824e-04 sample86 0.0969487314 -1.699897e-02 sample87 0.0421957457 -1.965953e-02 sample88 0.0215934743 1.566050e-02 sample89 0.0751559502 2.811652e-02 sample90 -0.0057328000 -8.283795e-03 sample91 -0.1134005268 -8.603522e-02 sample92 -0.0101689918 -6.894992e-02 sample93 0.0725967502 -6.003176e-03 sample94 -0.0096878852 -4.693081e-03 sample95 -0.0223502239 -3.139636e-02 sample96 -0.0013232863 -1.963604e-02 sample97 -0.0476541710 1.183660e-02 sample98 0.0269546160 -5.978398e-03 sample99 0.0728179461 4.597884e-02 sample100 -0.0413398038 1.079347e-02 sample101 0.0087536994 -6.796076e-02 sample102 0.0032509529 3.932612e-03 sample103 0.0360342395 -3.973263e-02 sample104 -0.0141722563 -2.453107e-02 sample105 0.0294940465 -7.140722e-03 sample106 0.0686472054 1.462895e-02 sample107 0.0748635927 8.401339e-03 sample108 0.0650175850 -6.211942e-03 sample109 -0.0628017242 -3.681224e-02 sample110 0.0905513691 -5.169053e-03 sample111 -0.0176679473 -3.884777e-02 sample112 0.0570870472 1.066018e-02 sample113 -0.0200110554 1.596044e-02 sample114 -0.0001474542 -3.679272e-02 sample115 -0.0213333038 -2.991667e-02 sample116 -0.0567675453 -2.785636e-02 sample117 -0.0379865990 -3.752078e-02 sample118 -0.0484878786 -9.173691e-03 sample119 -0.0713511831 -9.598634e-02 sample120 -0.0555093586 1.089843e-02 sample121 0.0542443861 3.861344e-02 sample122 0.0178575357 3.027138e-02 sample123 0.0775020581 -1.636852e-02 sample124 -0.0460701050 1.814758e-02 sample125 0.0543846585 2.075898e-03 sample126 -0.0729417144 3.276659e-02 sample127 -0.0609509157 -3.270814e-03 sample128 0.0908136899 3.758801e-02 sample129 0.0552445878 -1.879062e-02 sample130 0.0007128089 -1.294308e-02 sample131 -0.0693311345 7.357082e-03 sample132 -0.0556565156 3.126995e-02 sample133 0.0375870104 -1.977240e-02 sample134 -0.1229130924 3.159495e-02 sample135 0.0555550315 -5.563250e-04 sample136 -0.0159768414 -2.046339e-02 sample137 -0.0412337694 -1.151652e-02 sample138 -0.0180604476 -2.526505e-02 sample139 -0.0465649201 1.040683e-02 sample140 0.0452288969 -1.876279e-02 sample141 -0.0189142561 2.247042e-02 sample142 0.0297545566 1.280524e-02 sample143 0.0064292003 -1.997706e-02 sample144 -0.0124284903 -6.369733e-03 sample145 -0.0377141491 5.066743e-02 sample146 -0.0296240067 -3.344465e-02 sample147 0.0726083535 -1.239968e-02 sample148 -0.0284795794 3.389732e-02 sample149 0.0082261455 -6.399305e-02 sample150 -0.0765013197 2.704021e-02 sample151 -0.0220567356 -1.178159e-02 sample152 0.0403422737 -2.714879e-02 sample153 0.0629117719 7.425085e-02 sample154 0.0551622927 -3.548984e-02 sample155 0.0654439133 -1.005306e-02 sample156 0.0209310714 -1.390213e-02 sample157 0.0851522597 6.577150e-03 sample158 0.0208354599 -4.663078e-03 sample159 -0.0498794349 1.913257e-02 sample160 0.0216074437 1.656579e-02 sample161 -0.0075742328 -2.455676e-02 sample162 0.0963663017 5.705881e-02 sample163 -0.1009542191 7.174224e-02 sample164 0.0109881996 1.026806e-03 sample165 -0.0053146157 -6.772855e-03 sample166 -0.0275757357 2.673084e-02 sample167 -0.0825048036 2.278863e-03 sample168 0.0486147429 1.793843e-02 sample169 0.0302506727 8.984253e-03 > o2plsRes@scores$common[[2]] ## Common scores for Block 2 [,1] [,2] sample1 -0.0621842115 -1.364509e-02 sample2 0.0944623785 9.720892e-03 sample3 0.0406196267 -2.236338e-02 sample4 -0.0229316496 -3.932487e-04 sample5 -0.0157330047 3.231033e-03 sample6 -0.0945794025 3.120720e-02 sample7 -0.0854427118 -1.052880e-02 sample8 -0.1376625920 4.286608e-02 sample9 -0.0377115311 -1.415134e-02 sample10 0.0035244506 1.280825e-02 sample11 0.0016639987 -1.717895e-02 sample12 -0.0781403168 1.884368e-02 sample13 0.0938400516 2.838858e-02 sample14 -0.0759839772 1.810989e-02 sample15 -0.0068340837 -2.705361e-03 sample16 -0.0590150849 4.757848e-02 sample17 0.1178805097 2.040526e-02 sample18 0.0767858320 1.756604e-02 sample19 0.0157112113 -2.172867e-02 sample20 0.0485318300 -2.327033e-02 sample21 0.0185928176 4.777095e-02 sample22 -0.0191358702 -2.329775e-02 sample23 -0.0672994194 -1.535656e-03 sample24 0.1047476642 5.935707e-02 sample25 0.0329844953 -1.358036e-02 sample26 0.1154952052 1.741529e-02 sample27 0.0133849853 -3.590922e-02 sample28 0.0821554039 2.042376e-02 sample29 -0.0567643690 -2.123848e-02 sample30 0.1016073931 -1.134728e-03 sample31 -0.0880396372 3.670548e-02 sample32 0.0300363338 1.182406e-02 sample33 -0.0467252272 3.739254e-03 sample34 0.0783666394 1.203777e-02 sample35 0.0424227097 -1.118559e-02 sample36 -0.1107646166 -1.143464e-02 sample37 -0.0191667664 -2.246060e-02 sample38 0.0155968095 -2.909621e-02 sample39 0.0746847148 7.148218e-03 sample40 -0.0517028178 -2.137267e-02 sample41 0.0234979494 -3.723018e-02 sample42 0.0388797356 -8.557228e-03 sample43 0.0149555568 7.210002e-03 sample44 -0.1150305613 3.461805e-02 sample45 0.0846146236 3.486020e-02 sample46 0.0884426404 -3.246853e-02 sample47 0.0748644971 -8.083045e-03 sample48 -0.0012033198 -9.403647e-03 sample49 -0.0872662737 3.616245e-02 sample50 0.0066941314 -5.284863e-02 sample51 -0.0411777630 3.791830e-02 sample52 -0.0379355780 2.180834e-02 sample53 -0.0851639886 4.751761e-02 sample54 0.0288006248 7.184424e-03 sample55 -0.0164920835 5.919925e-05 sample56 0.0355115616 1.951043e-02 sample57 -0.0141146068 3.492409e-02 sample58 -0.0015636132 9.862883e-03 sample59 -0.0390656483 3.590929e-03 sample60 -0.0139454780 3.963030e-03 sample61 -0.0106410274 1.919705e-02 sample62 0.0236748439 -5.922677e-03 sample63 -0.0846790877 3.839102e-02 sample64 -0.1202581015 2.846469e-02 sample65 0.0050548584 6.328644e-03 sample66 0.0028013072 1.291807e-02 sample67 -0.1231623009 -2.112565e-02 sample68 -0.0437782161 -2.845072e-02 sample69 -0.0501199692 2.053469e-03 sample70 -0.0140278645 -2.027157e-02 sample71 0.0057489505 -4.085977e-02 sample72 0.0511212704 -5.522408e-03 sample73 0.0828141409 7.431582e-03 sample74 -0.0085959456 1.772951e-02 sample75 -0.0312180394 -6.636869e-03 sample76 -0.0519051781 -1.640191e-02 sample77 -0.0925924762 -6.907800e-03 sample78 0.1163971046 2.251122e-02 sample79 -0.0240906926 -4.887766e-02 sample80 -0.0221327065 -6.730703e-03 sample81 -0.0072114968 -2.254399e-02 sample82 0.1204416674 -9.907422e-03 sample83 0.0386739485 -1.171663e-03 sample84 0.0195988488 -1.033806e-02 sample85 -0.0877680171 -1.725057e-03 sample86 0.1023541048 -1.062501e-02 sample87 0.0425213089 -1.356865e-02 sample88 0.0244788514 1.180820e-02 sample89 0.0804276691 2.188588e-02 sample90 -0.0074639871 -6.140721e-03 sample91 -0.1278832404 -6.485140e-02 sample92 -0.0162199697 -5.048358e-02 sample93 0.0769344893 -3.045135e-03 sample94 -0.0104345587 -3.593172e-03 sample95 -0.0260058453 -2.330475e-02 sample96 -0.0025018700 -1.433516e-02 sample97 -0.0492358305 7.774183e-03 sample98 0.0279220220 -3.862141e-03 sample99 0.0813921923 3.487339e-02 sample100 -0.0428797405 7.112807e-03 sample101 0.0032855240 -4.940743e-02 sample102 0.0038439317 2.938008e-03 sample103 0.0358511139 -2.831881e-02 sample104 -0.0162784000 -1.815061e-02 sample105 0.0314853405 -4.656633e-03 sample106 0.0726456731 1.192390e-02 sample107 0.0807342975 7.508627e-03 sample108 0.0688338003 -3.336161e-03 sample109 -0.0694151950 -2.800146e-02 sample110 0.0961218924 -2.111997e-03 sample111 -0.0217900036 -2.864702e-02 sample112 0.0599954082 8.820317e-03 sample113 -0.0195006577 1.128215e-02 sample114 -0.0032126533 -2.682851e-02 sample115 -0.0251101087 -2.221077e-02 sample116 -0.0625141551 -2.137258e-02 sample117 -0.0440473375 -2.806256e-02 sample118 -0.0532042630 -7.590494e-03 sample119 -0.0848603028 -7.133574e-02 sample120 -0.0588832131 6.937326e-03 sample121 0.0613899126 2.915307e-02 sample122 0.0218424338 2.241775e-02 sample123 0.0809008460 -1.051759e-02 sample124 -0.0472109313 1.239887e-02 sample125 0.0583180947 2.521167e-03 sample126 -0.0753941872 2.256455e-02 sample127 -0.0649774209 -3.496964e-03 sample128 0.1000212216 2.908091e-02 sample129 0.0568033049 -1.269016e-02 sample130 -0.0002370832 -9.419675e-03 sample131 -0.0727030877 4.091672e-03 sample132 -0.0566219024 2.179861e-02 sample133 0.0384172955 -1.372840e-02 sample134 -0.1280862736 2.077912e-02 sample135 0.0592633273 6.106685e-04 sample136 -0.0187635410 -1.521173e-02 sample137 -0.0449958970 -9.152840e-03 sample138 -0.0211348699 -1.875415e-02 sample139 -0.0482882861 6.729304e-03 sample140 0.0468926306 -1.285498e-02 sample141 -0.0186248693 1.605439e-02 sample142 0.0328031246 9.887746e-03 sample143 0.0052919839 -1.445666e-02 sample144 -0.0140067923 -4.867248e-03 sample145 -0.0361804310 3.625323e-02 sample146 -0.0345286735 -2.493652e-02 sample147 0.0765025670 -7.714769e-03 sample148 -0.0276016641 2.420589e-02 sample149 0.0027545308 -4.653007e-02 sample150 -0.0792296010 1.831289e-02 sample151 -0.0245894512 -8.991738e-03 sample152 0.0409796547 -1.907063e-02 sample153 0.0734301757 5.528780e-02 sample154 0.0557740684 -2.487723e-02 sample155 0.0689436560 -6.127635e-03 sample156 0.0212272938 -9.747423e-03 sample157 0.0911931194 6.355708e-03 sample158 0.0220840645 -3.016357e-03 sample159 -0.0513244242 1.304175e-02 sample160 0.0246213576 1.248444e-02 sample161 -0.0100369130 -1.805391e-02 sample162 0.1078802043 4.337260e-02 sample163 -0.1017965082 5.047171e-02 sample164 0.0119430799 9.593002e-04 sample165 -0.0063708014 -5.032148e-03 sample166 -0.0283181180 1.899222e-02 sample167 -0.0872832229 1.516582e-04 sample168 0.0540714512 1.397701e-02 sample169 0.0328432652 7.104347e-03 > o2plsRes@scores$dist[[1]] ## Distinctive scores for Block 1 [,1] [,2] sample1 0.0133684846 2.195848e-02 sample2 0.0254157197 -1.058416e-02 sample3 -0.0049551479 -4.840017e-03 sample4 0.0310390570 -1.063929e-02 sample5 0.0046941318 -6.488426e-03 sample6 -0.0107406753 -1.026702e-02 sample7 -0.0225157631 2.624712e-04 sample8 0.0141320952 -9.505821e-03 sample9 0.0029681280 2.078210e-02 sample10 0.0131729174 -2.275042e-03 sample11 -0.0004164298 1.994019e-02 sample12 -0.0095211620 3.759883e-02 sample13 0.0091018604 -7.953956e-03 sample14 -0.0106557524 -9.181659e-03 sample15 -0.0249924121 3.262724e-02 sample16 -0.0156216400 1.375700e-02 sample17 -0.0019382446 1.073994e-03 sample18 -0.0221072481 -8.703592e-03 sample19 0.0146917619 -1.311712e-02 sample20 -0.0160353760 1.826290e-02 sample21 0.0035947899 -9.616341e-03 sample22 -0.0225060762 -2.532589e-03 sample23 0.0310000683 3.033060e-03 sample24 0.0499544372 1.809450e-02 sample25 0.0284442301 -1.932558e-02 sample26 0.0188220043 2.146985e-02 sample27 -0.0257763219 -1.999228e-03 sample28 0.0120888648 1.125834e-02 sample29 -0.0236482520 4.426726e-02 sample30 -0.0385486305 -2.055935e-02 sample31 -0.0181539336 -5.877838e-03 sample32 -0.0302630460 -2.607192e-03 sample33 -0.0319565715 -1.562628e-02 sample34 -0.0197970124 9.906813e-03 sample35 -0.0247412713 -5.434440e-03 sample36 -0.0386259060 -3.190394e-02 sample37 -0.0566199273 -4.192574e-02 sample38 -0.0142060273 2.259644e-02 sample39 0.0053589035 1.076485e-02 sample40 -0.0552546493 -3.819896e-02 sample41 -0.0013089975 9.278818e-05 sample42 0.0137252142 -1.664652e-02 sample43 -0.0151259626 -6.290953e-03 sample44 0.0617391754 -1.442883e-02 sample45 0.0231410886 1.163143e-03 sample46 -0.0148898209 -1.384176e-04 sample47 -0.0187252536 1.221690e-02 sample48 0.0432839432 1.416671e-02 sample49 0.0160818605 -3.588745e-02 sample50 0.0059333545 4.067003e-02 sample51 -0.0142914866 7.776270e-03 sample52 -0.0086339952 7.208917e-03 sample53 -0.0207386980 6.272432e-03 sample54 -0.0039856719 -1.316934e-02 sample55 -0.0056217017 5.692315e-03 sample56 0.0000123292 8.978290e-04 sample57 -0.0095805555 1.324253e-02 sample58 -0.0124160295 -7.326376e-03 sample59 -0.0400195442 -1.349736e-02 sample60 -0.0460063358 2.770091e-02 sample61 -0.0245266456 1.470710e-02 sample62 -0.0366022783 -3.437352e-03 sample63 0.0013742171 3.288796e-02 sample64 -0.0070599859 2.739588e-02 sample65 0.0041201911 1.498268e-02 sample66 0.0143173351 -1.968812e-02 sample67 -0.0467477531 -1.929938e-02 sample68 -0.0306751978 -1.436184e-02 sample69 -0.0125317217 4.130407e-03 sample70 -0.0068071487 8.080857e-03 sample71 0.0169170264 -7.027348e-03 sample72 -0.0346909749 -1.333770e-02 sample73 -0.0280506153 1.493843e-02 sample74 -0.0182611498 3.294697e-03 sample75 -0.0120563964 8.974612e-03 sample76 0.0001437236 -4.253184e-02 sample77 0.0065330299 -5.252886e-02 sample78 0.0288278141 -1.127782e-02 sample79 0.0503961481 -1.023318e-02 sample80 -0.0207693429 3.648391e-02 sample81 0.0163562768 -9.074596e-03 sample82 -0.0084317129 -1.478976e-02 sample83 -0.0474097918 -1.103126e-02 sample84 0.0177181395 -7.191197e-03 sample85 -0.0342718548 -3.082360e-02 sample86 -0.0261671791 -1.089491e-02 sample87 -0.0009486358 -2.411514e-02 sample88 0.0020528931 -2.894615e-02 sample89 -0.0189361111 -2.638639e-03 sample90 -0.0009863658 -2.390075e-02 sample91 -0.0124352695 8.153234e-02 sample92 0.0564264106 -8.909537e-03 sample93 -0.0081461774 1.570851e-02 sample94 -0.0054896581 1.547251e-02 sample95 0.0224073150 -4.374348e-04 sample96 0.0173528924 -3.050441e-03 sample97 0.0067948115 5.008237e-03 sample98 -0.0116030825 1.498764e-02 sample99 0.0246422688 -4.054795e-03 sample100 -0.0069420745 -4.846343e-04 sample101 0.0124923691 3.091503e-02 sample102 0.0650835386 -1.367400e-02 sample103 -0.0042741828 7.855985e-03 sample104 0.0250591040 -4.171938e-03 sample105 0.0157516368 -3.121990e-02 sample106 0.0060593853 -5.101693e-03 sample107 -0.0098329626 1.044506e-02 sample108 0.0044269853 4.142036e-03 sample109 0.0572473486 1.517542e-02 sample110 0.0090474827 -5.119868e-03 sample111 0.0444263015 7.983232e-03 sample112 -0.0131765484 -9.696342e-04 sample113 0.0241047399 6.706740e-03 sample114 0.0074558775 -4.728652e-03 sample115 0.0611851433 1.117210e-02 sample116 0.0432646951 -1.380556e-02 sample117 0.0516750066 -3.575617e-02 sample118 0.0139942100 -3.279138e-03 sample119 0.0291722987 5.587946e-02 sample120 0.0103515853 -1.690016e-03 sample121 -0.0091396331 3.552116e-02 sample122 0.0260431679 -7.583975e-03 sample123 -0.0076666389 -1.628489e-02 sample124 0.0283466326 3.127845e-03 sample125 0.0016472378 -2.770692e-02 sample126 -0.0286529417 3.489336e-02 sample127 -0.0010224500 7.483214e-03 sample128 0.0209049296 2.572016e-02 sample129 -0.0218184878 -1.755347e-02 sample130 -0.0005009620 -1.697978e-02 sample131 -0.0134032968 4.637390e-03 sample132 0.0198526786 5.723983e-04 sample133 0.0088812957 -9.988115e-03 sample134 -0.0137484514 1.172591e-02 sample135 -0.0220314568 1.347465e-02 sample136 -0.0185173353 5.168079e-03 sample137 -0.0248352123 -9.472788e-03 sample138 0.0301635767 -1.175283e-02 sample139 -0.0173576929 -3.872592e-02 sample140 -0.0262157762 2.456863e-02 sample141 0.0058369763 -1.420854e-02 sample142 0.0207886071 -1.188764e-02 sample143 0.0092832598 -1.324238e-02 sample144 0.0028442140 3.627979e-03 sample145 0.0199749569 2.862202e-03 sample146 -0.0182236697 1.726556e-03 sample147 -0.0282519995 -2.825595e-02 sample148 0.0065435868 -1.572917e-02 sample149 0.0158233820 -2.159451e-02 sample150 -0.0177383738 -3.020633e-03 sample151 0.0245166984 -6.888241e-03 sample152 0.0107259913 3.314630e-02 sample153 0.0550963965 3.758760e-02 sample154 -0.0131452472 -8.153903e-04 sample155 -0.0211742574 2.642246e-03 sample156 -0.0117803505 2.698265e-02 sample157 -0.0096167165 1.433840e-02 sample158 -0.0101754772 9.137620e-03 sample159 0.0120662931 -2.565236e-02 sample160 -0.0132238202 2.916023e-03 sample161 0.0274491966 -1.748284e-02 sample162 0.0012482909 3.152261e-02 sample163 0.0042031315 1.830701e-02 sample164 0.0174896157 -1.175915e-02 sample165 0.0097517662 -6.119019e-03 sample166 0.0190134679 -1.121582e-02 sample167 -0.0044140836 4.665585e-03 sample168 0.0049689168 -1.941822e-02 sample169 -0.0209802098 3.498729e-03 > o2plsRes@scores$dist[[2]] ## Distinctive scores for Block 2 [,1] [,2] sample1 -0.0515543627 -0.0305856787 sample2 -0.0144993256 0.0236342950 sample3 -0.0371833108 -0.0140263348 sample4 0.0068945388 -0.0132539692 sample5 0.0215035333 -0.0663338101 sample6 -0.0187055152 0.0088773016 sample7 -0.0061521552 0.0064029054 sample8 -0.0210874459 0.0334652901 sample9 0.0516865043 -0.0291142799 sample10 0.0059440366 -0.0527217447 sample11 0.0393010793 -0.0200624712 sample12 -0.0420837100 0.0131331362 sample13 0.0333252565 0.0818552509 sample14 -0.0190062644 0.0160202175 sample15 -0.0030968049 -0.0189230681 sample16 -0.0004452158 0.0018880102 sample17 -0.0185848615 0.0240170131 sample18 -0.0273093598 0.0230213640 sample19 -0.0217761111 -0.0445894441 sample20 0.0245820821 0.0159812738 sample21 0.0034527644 -0.0400016054 sample22 -0.0340789054 0.0039289109 sample23 -0.0010344929 -0.0310161212 sample24 0.0289468503 0.0760962436 sample25 -0.0119098496 -0.0122798760 sample26 -0.0181001057 0.0517892852 sample27 0.0050465417 -0.0086515844 sample28 0.0057491502 0.0358830107 sample29 -0.0051104246 0.0116605117 sample30 -0.0103085904 0.0039678538 sample31 -0.0319929858 0.0090606113 sample32 -0.0036232521 -0.0328202010 sample33 -0.0534742153 0.0024751837 sample34 -0.0067495749 -0.0111000311 sample35 0.0378745721 0.0465929296 sample36 0.0647886800 0.0359987924 sample37 0.0488441236 0.0492906912 sample38 -0.0251514062 0.0197110110 sample39 -0.0085428066 -0.0105117852 sample40 0.0379324087 0.0440810741 sample41 -0.0044199152 -0.0128820644 sample42 -0.0292553573 -0.0067045265 sample43 -0.0077829155 -0.0510178219 sample44 0.0045122248 0.0479660309 sample45 -0.0074444298 -0.0051116726 sample46 -0.0088025512 0.0196186661 sample47 0.0076696301 0.0215947965 sample48 0.0290108585 -0.0175568376 sample49 -0.0141754858 0.0184717099 sample50 0.0006282201 -0.0233054373 sample51 0.0441995177 -0.0410022921 sample52 0.0715329391 -0.0399499475 sample53 -0.0095954087 -0.0029140909 sample54 0.0048933768 -0.0281884386 sample55 0.0327325487 -0.0532290012 sample56 0.0323068984 -0.0256595538 sample57 0.0806603122 -0.0286748097 sample58 -0.0064792049 -0.0006945349 sample59 0.0088958941 0.0067389649 sample60 0.0874124612 0.0431964341 sample61 0.0577604571 -0.0326112099 sample62 -0.0313318464 0.0224391756 sample63 -0.0233625220 0.0125110562 sample64 -0.0086426068 0.0148770341 sample65 0.0025256193 -0.0404466327 sample66 0.0006014071 -0.0471576264 sample67 0.0706087042 0.0516228406 sample68 0.0082301011 0.0033109509 sample69 -0.0475076743 0.0001452708 sample70 -0.0600773716 0.0089986962 sample71 -0.0096321627 -0.0050761187 sample72 -0.0031773546 -0.0166221542 sample73 -0.0113700517 -0.0191726684 sample74 -0.0014179662 -0.0608101325 sample75 0.0041911740 -0.0399981269 sample76 -0.0055326449 0.0353114263 sample77 -0.0260214459 0.0305731380 sample78 -0.0119267436 0.0632236007 sample79 0.0186017239 0.0027402910 sample80 0.0241047889 -0.0472697181 sample81 -0.0220288317 -0.0079577210 sample82 -0.0180751258 0.0639051029 sample83 -0.0256671713 -0.0125898269 sample84 0.0161392598 -0.0567222449 sample85 0.0139988188 0.0322763454 sample86 -0.0198382995 0.0389225776 sample87 0.0266270281 -0.0032979996 sample88 0.0515677078 0.0117902495 sample89 0.0014022125 -0.0140510488 sample90 -0.0375949749 0.0044004551 sample91 0.0310397965 0.0440610926 sample92 0.0270570567 0.0324380452 sample93 -0.0215009202 0.0063993941 sample94 -0.0415702912 -0.0037692077 sample95 -0.0168416047 0.0010019120 sample96 -0.0285582661 -0.0187991000 sample97 -0.0490843868 -0.0266760748 sample98 -0.0171579033 -0.0112897471 sample99 -0.0271316525 0.0232395583 sample100 -0.0301789816 0.0305498693 sample101 -0.0264371151 0.0170723968 sample102 0.0012767734 -0.0248949597 sample103 0.0055214687 -0.0030040587 sample104 0.0251346074 -0.0165212671 sample105 0.0062424215 -0.0400309901 sample106 0.0069768684 0.0154982315 sample107 -0.0315912602 -0.0118883820 sample108 -0.0109690679 0.0023637162 sample109 -0.0014762845 0.0165583675 sample110 0.0036971063 0.0168260726 sample111 -0.0071624739 -0.0345651461 sample112 0.0046098120 -0.0048009350 sample113 0.0082236008 -0.0383233357 sample114 -0.0293642209 -0.0165595240 sample115 -0.0003260453 0.0135805368 sample116 0.0183575759 0.0665377581 sample117 0.0227640036 -0.0012287760 sample118 0.0015695248 0.0472617382 sample119 0.0190084932 0.0590034062 sample120 -0.0449645755 0.0072755697 sample121 0.0077307184 0.0104738937 sample122 -0.0027132063 -0.0394983138 sample123 0.0016959300 0.0028593594 sample124 -0.0365091615 0.0040382925 sample125 -0.0053658663 -0.0316029164 sample126 -0.0458032408 0.0019165544 sample127 -0.0494064872 0.0088209044 sample128 -0.0155454766 0.0186819802 sample129 -0.0184340400 0.0038684312 sample130 -0.0303640987 -0.0052225766 sample131 -0.0088697422 0.0156339713 sample132 -0.0433916471 -0.0154075483 sample133 0.0204029276 -0.0282209049 sample134 0.0175513332 0.0262883962 sample135 0.0029009925 0.0017003151 sample136 -0.0367997573 -0.0072249751 sample137 -0.0348600323 0.0075400273 sample138 -0.0044063824 -0.0053752428 sample139 0.0073103935 0.0308956174 sample140 0.0039925654 -0.0167019605 sample141 -0.0184093462 -0.0387953445 sample142 0.0268670676 -0.0239229634 sample143 0.0421049126 -0.0110888235 sample144 0.0017253664 -0.0341766012 sample145 0.0681741320 -0.0073526377 sample146 -0.0239965222 0.0118396767 sample147 -0.0063453522 0.0183130585 sample148 0.0230825251 -0.0379753037 sample149 0.0223298673 0.0188909118 sample150 0.0055709108 0.0174179009 sample151 0.0039177786 -0.0233533275 sample152 0.0134325667 0.0302344591 sample153 0.0511990309 0.0730230140 sample154 0.0006698324 0.0154177486 sample155 0.0032926626 -0.0288651601 sample156 -0.0016463495 -0.0474657733 sample157 -0.0045857599 0.0154934573 sample158 0.0201775524 -0.0332982124 sample159 -0.0086909001 0.0073496711 sample160 0.0295437331 -0.0555734536 sample161 0.0332754288 0.0033779619 sample162 0.0121954537 0.0433540412 sample163 -0.0173490933 0.0227219128 sample164 0.0143374783 -0.0453542590 sample165 0.0343612593 -0.0511194536 sample166 -0.0157536004 0.0094621170 sample167 -0.0179654624 -0.0006982358 sample168 -0.0033829919 0.0060747155 sample169 0.0116231468 -0.0015112800 > > ## 3.3 Plotting VAF > > # DISCO-SCA plotVAF > plotVAF(discoRes) > > # JIVE plotVAF > plotVAF(jiveRes) > > > ######################### > ## PART 4. Plot Results > > # Scores for common part. DISCO-SCA > plotRes(object=discoRes,comps=c(1,2),what="scores",type="common", + combined=FALSE,block=NULL,color="classname",shape=NULL,labels=NULL, + background=TRUE,palette=NULL,pointSize=4,labelSize=NULL, + axisSize=NULL,titleSize=NULL) > > # Scores for common part. JIVE > plotRes(object=jiveRes,comps=c(1,2),what="scores",type="common", + combined=FALSE,block=NULL,color="classname",shape=NULL,labels=NULL, + background=TRUE,palette=NULL,pointSize=4,labelSize=NULL, + axisSize=NULL,titleSize=NULL) > > # Scores for common part. O2PLS. > p1 <- plotRes(object=o2plsRes,comps=c(1,2),what="scores",type="common", + combined=FALSE,block="expr",color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > p2 <- plotRes(object=o2plsRes,comps=c(1,2),what="scores",type="common", + combined=FALSE,block="mirna",color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > legend <- g_legend(p1) > grid.arrange(arrangeGrob(p1+theme(legend.position="none"), + p2+theme(legend.position="none"),nrow=1), + legend,heights=c(6/7,1/7)) > > # Combined plot of scores for common part. O2PLS. > plotRes(object=o2plsRes,comps=c(1,1),what="scores",type="common", + combined=TRUE,block=NULL,color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > > > # Scores for distinctive part. DISCO-SCA. (two plots one for each block) > p1 <- plotRes(object=discoRes,comps=c(1,2),what="scores",type="individual", + combined=FALSE,block="expr",color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > p2 <- plotRes(object=discoRes,comps=c(1,2),what="scores",type="individual", + combined=FALSE,block="mirna",color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > legend <- g_legend(p1) > grid.arrange(arrangeGrob(p1+theme(legend.position="none"), + p2+theme(legend.position="none"),nrow=1), + legend,heights=c(6/7,1/7)) > > # Combined plot of scores for distinctive part. DISCO-SCA > plotRes(object=discoRes,comps=c(1,1),what="scores",type="individual", + combined=TRUE,block=NULL,color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > > # Combined plot of scores for common and distinctive part. O2PLS (two plots one for each block) > p1 <- plotRes(object=o2plsRes,comps=c(1,1),what="scores",type="both", + combined=FALSE,block="expr",color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > p2 <- plotRes(object=o2plsRes,comps=c(1,1),what="scores",type="both", + combined=FALSE,block="mirna",color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > legend <- g_legend(p1) > grid.arrange(arrangeGrob(p1+theme(legend.position="none"), + p2+theme(legend.position="none"),nrow=1), + legend,heights=c(6/7,1/7)) > > # Combined plot of scores for common and distinctive part. DISCO (two plots one for each block) > p1 <- plotRes(object=discoRes,comps=c(1,1),what="scores",type="both", + combined=FALSE,block="expr",color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > p2 <- plotRes(object=discoRes,comps=c(1,1),what="scores",type="both", + combined=FALSE,block="mirna",color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > legend <- g_legend(p1) > grid.arrange(arrangeGrob(p1+theme(legend.position="none"), + p2+theme(legend.position="none"),nrow=1), + legend,heights=c(6/7,1/7)) > > # Loadings for common part. DISCO-SCA. (two plots one for each block) > p1 <- plotRes(object=discoRes,comps=c(1,2),what="loadings",type="common", + combined=FALSE,block="expr",color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > p2 <- plotRes(object=discoRes,comps=c(1,2),what="loadings",type="common", + combined=FALSE,block="mirna",color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > grid.arrange(arrangeGrob(p1+theme(legend.position="none"), + p2+theme(legend.position="none"),nrow=1), + heights=c(6/7,1/7)) > > > # Loadings for distinctive part. DISCO-SCA. (two plots one for each block) > p1 <- plotRes(object=discoRes,comps=c(1,2),what="loadings",type="individual", + combined=FALSE,block="expr",color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > p2 <- plotRes(object=discoRes,comps=c(1,2),what="loadings",type="individual", + combined=FALSE,block="mirna",color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > grid.arrange(arrangeGrob(p1+theme(legend.position="none"), + p2+theme(legend.position="none"),nrow=1), + heights=c(6/7,1/7)) > > > # Combined plot for loadings from common and distinctive part (two plots one for each block) > p1 <- plotRes(object=discoRes,comps=c(1,1),what="loadings",type="both", + combined=FALSE,block="expr",color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > p2 <- plotRes(object=discoRes,comps=c(1,1),what="loadings",type="both", + combined=FALSE,block="mirna",color="classname",shape=NULL, + labels=NULL,background=TRUE,palette=NULL,pointSize=4, + labelSize=NULL,axisSize=NULL,titleSize=NULL) > grid.arrange(arrangeGrob(p1+theme(legend.position="none"), + p2+theme(legend.position="none"),nrow=1), + heights=c(6/7,1/7)) > > > > ## Plot scores and loadings togheter: Common components DISCO-SCA > p1 <- plotRes(object=discoRes,comps=c(1,2),what="both",type="common", + combined=FALSE,block="expr",color="classname",shape=NULL,labels=NULL, + background=TRUE,palette=NULL,pointSize=4,labelSize=NULL, + axisSize=NULL,titleSize=NULL) > p2 <- plotRes(object=discoRes,comps=c(1,2),what="both",type="common", + combined=FALSE,block="mirna",color="classname",shape=NULL,labels=NULL, + background=TRUE,palette=NULL,pointSize=4,labelSize=NULL, + axisSize=NULL,titleSize=NULL) > grid.arrange(arrangeGrob(p1+theme(legend.position="none"), + p2+theme(legend.position="none"),nrow=1), + heights=c(6/7,1/7)) > > > ## Plot scores and loadings togheter: Common components O2PLS > p1 <- plotRes(object=o2plsRes,comps=c(1,2),what="both",type="common", + combined=FALSE,block="expr",color="classname",shape=NULL,labels=NULL, + background=TRUE,palette=NULL,pointSize=4,labelSize=NULL, + axisSize=NULL,titleSize=NULL) > p2 <- plotRes(object=o2plsRes,comps=c(1,2),what="both",type="common", + combined=FALSE,block="mirna",color="classname",shape=NULL,labels=NULL, + background=TRUE,palette=NULL,pointSize=4,labelSize=NULL, + axisSize=NULL,titleSize=NULL) > grid.arrange(arrangeGrob(p1+theme(legend.position="none"), + p2+theme(legend.position="none"),nrow=1), + heights=c(6/7,1/7)) > > > ## Plot scores and loadings togheter: Distintive components DISCO-SCA > p1 <- plotRes(object=discoRes,comps=c(1,2),what="both",type="individual", + combined=FALSE,block="expr",color="classname",shape=NULL,labels=NULL, + background=TRUE,palette=NULL,pointSize=4,labelSize=NULL, + axisSize=NULL,titleSize=NULL) > p2 <- plotRes(object=discoRes,comps=c(1,2),what="both",type="individual", + combined=FALSE,block="mirna",color="classname",shape=NULL,labels=NULL, + background=TRUE,palette=NULL,pointSize=4,labelSize=NULL, + axisSize=NULL,titleSize=NULL) > grid.arrange(arrangeGrob(p1+theme(legend.position="none"), + p2+theme(legend.position="none"),nrow=1), + heights=c(6/7,1/7)) > > > > > proc.time() user system elapsed 11.486 0.280 11.757
STATegRa.Rcheck/STATegRa-Ex.timings
name | user | system | elapsed | |
STATegRaUsersGuide | 0.001 | 0.000 | 0.001 | |
STATegRa_data | 0.228 | 0.004 | 0.231 | |
STATegRa_data_TCGA_BRCA | 0.002 | 0.000 | 0.002 | |
bioDist | 0.397 | 0.044 | 0.441 | |
bioDistFeature | 0.297 | 0.012 | 0.309 | |
bioDistFeaturePlot | 0.327 | 0.020 | 0.347 | |
bioDistW | 0.314 | 0.008 | 0.322 | |
bioDistWPlot | 0.316 | 0.000 | 0.316 | |
bioMap | 0.003 | 0.000 | 0.003 | |
combiningMappings | 0.008 | 0.004 | 0.010 | |
createOmicsExpressionSet | 0.133 | 0.004 | 0.137 | |
getInitialData | 0.554 | 0.021 | 0.575 | |
getLoadings | 0.639 | 0.038 | 0.677 | |
getMethodInfo | 0.677 | 0.008 | 0.685 | |
getPreprocessing | 0.815 | 0.608 | 1.421 | |
getScores | 0.684 | 0.052 | 0.736 | |
getVAF | 0.591 | 0.000 | 0.591 | |
holistOmics | 0.000 | 0.003 | 0.002 | |
modelSelection | 1.499 | 1.661 | 3.160 | |
omicsCompAnalysis | 4.066 | 0.112 | 4.178 | |
omicsNPC | 0.000 | 0.002 | 0.002 | |
plotRes | 4.514 | 0.061 | 4.575 | |
plotVAF | 4.208 | 0.040 | 4.248 | |