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This page was generated on 2022-01-14 13:08:41 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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

CHECK results for STATegRa on machv2


To the developers/maintainers of the STATegRa package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1887/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STATegRa 1.30.0  (landing page)
David Gomez-Cabrero , Núria Planell
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/STATegRa
git_branch: RELEASE_3_14
git_last_commit: 9124807
git_last_commit_date: 2021-10-26 12:17:04 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: STATegRa
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:STATegRa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings STATegRa_1.30.0.tar.gz
StartedAt: 2022-01-13 18:38:34 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 18:43:47 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 313.1 seconds
RetCode: 0
Status:   OK  
CheckDir: STATegRa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:STATegRa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings STATegRa_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/STATegRa.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘STATegRa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STATegRa’ version ‘1.30.0’
* 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 R 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 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
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plotRes           7.548  0.166   7.721
plotVAF           6.120  0.161   6.290
omicsCompAnalysis 5.643  0.234   5.884
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/STATegRa.Rcheck/00check.log’
for details.



Installation output

STATegRa.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL STATegRa
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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)

Tests output

STATegRa.Rcheck/tests/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 -- Thu Jan 13 18:43:38 2022 
*********************************************** 
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 
  4.731   0.323   5.039 

STATegRa.Rcheck/tests/STATEgRa_Example.omicsCLUST.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.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(...) :
  relative range of values (   0 * EPS) is small (axis 2)
5: In plot.window(...) :
  relative range of values (   0 * EPS) is small (axis 2)
6: In plot.window(...) :
  relative range of values (   0 * EPS) is small (axis 2)
7: In plot.window(...) :
  relative range of values (   0 * EPS) is small (axis 2)
> 
> #############################################
> ## 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 
 36.847   0.869  37.734 

STATegRa.Rcheck/tests/STATegRa_Example.omicsNPC.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 
121.015   1.635 122.748 

STATegRa.Rcheck/tests/STATEgRa_Example.omicsPCA.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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    0.0781575619 -0.0431548737
sample2   -0.1192221365  0.0294021598
sample3   -0.0531408697 -0.0746837599
sample4    0.0292971796 -0.0006034225
sample5    0.0202090753  0.0110455234
sample6    0.1226088451  0.1053493273
sample7    0.1078931328 -0.0322418892
sample8    0.1782891157  0.1449330304
sample9    0.0468697290 -0.0455171704
sample10  -0.0036032679  0.0420077660
sample11  -0.0035566366 -0.0566285088
sample12   0.1006129677  0.0641394089
sample13  -0.1174412792  0.0907475359
sample14   0.0981203558  0.0617763675
sample15   0.0085337249 -0.0086955899
sample16   0.0783146826  0.1581333682
sample17  -0.1483610663  0.0638580124
sample18  -0.0963084399  0.0556688162
sample19  -0.0217243077 -0.0720128804
sample20  -0.0635633942 -0.0779610018
sample21  -0.0201843980  0.1566381954
sample22   0.0218273826 -0.0764055569
sample23   0.0852039055 -0.0032765388
sample24  -0.1287181468  0.1924425639
sample25  -0.0430575637 -0.0456639003
sample26  -0.1453899774  0.0541458558
sample27  -0.0197483631 -0.1185592513
sample28  -0.1025339414  0.0650655194
sample29   0.0706022444 -0.0682932627
sample30  -0.1295622993 -0.0066677149
sample31   0.1147449312  0.1232727488
sample32  -0.0374308219  0.0380249981
sample33   0.0599520754  0.0136936521
sample34  -0.0984199310  0.0375364864
sample35  -0.0543096424 -0.0378034777
sample36   0.1403628042 -0.0343638287
sample37   0.0228947664 -0.0732688706
sample38  -0.0222073041 -0.0962567065
sample39  -0.0941739217  0.0215180434
sample40   0.0643807063 -0.0687718986
sample41  -0.0327634987 -0.1232187200
sample42  -0.0500431634 -0.0292514017
sample43  -0.0184497186  0.0233044589
sample44   0.1487889376  0.1171209310
sample45  -0.1050778780  0.1123140016
sample46  -0.1151191610 -0.1093995569
sample47  -0.0962591533 -0.0288417755
sample48   0.0004832626 -0.0310380013
sample49   0.1135203887  0.1213936382
sample50  -0.0123549936 -0.1740763066
sample51   0.0550527449  0.1258931056
sample52   0.0499118498  0.0728581178
sample53   0.1119772673  0.1588064608
sample54  -0.0360055715  0.0228585696
sample55   0.0210418831  0.0006750842
sample56  -0.0434171488  0.0633131299
sample57   0.0197820705  0.1150754209
sample58   0.0030440704  0.0326127747
sample59   0.0500256735  0.0129522283
sample60   0.0184280087  0.0136218935
sample61   0.0150298926  0.0635097391
sample62  -0.0304758763 -0.0201235587
sample63   0.1102250127  0.1285968322
sample64   0.1552586833  0.0971185353
sample65  -0.0058503817  0.0207102655
sample66  -0.0025607465  0.0424284347
sample67   0.1546638666 -0.0661577323
sample68   0.0536374244 -0.0923603585
sample69   0.0640332992  0.0082004000
sample70   0.0163521726 -0.0663227181
sample71  -0.0102536123 -0.1345965213
sample72  -0.0654191761 -0.0196035675
sample73  -0.1048553249  0.0221000448
sample74   0.0123800504  0.0586157152
sample75   0.0392079734 -0.0209725993
sample76   0.0648954574 -0.0524759444
sample77   0.1172922649 -0.0201200436
sample78  -0.1463072612  0.0708399091
sample79   0.0265208838 -0.1603426191
sample80   0.0279739213 -0.0214153020
sample81   0.0079212147 -0.0738495791
sample82  -0.1544234602 -0.0361450468
sample83  -0.0494205425 -0.0049938186
sample84  -0.0259039728 -0.0346591848
sample85   0.1116487442 -0.0031403568
sample86  -0.1306479061 -0.0377155587
sample87  -0.0554777863 -0.0459739575
sample88  -0.0301626520  0.0382206777
sample89  -0.1016866188  0.0694078526
sample90   0.0086821638 -0.0201323833
sample91   0.1578629762 -0.2097791964
sample92   0.0170933511 -0.1655937220
sample93  -0.0979805103 -0.0121500389
sample94   0.0131486213 -0.0114929443
sample95   0.0315682459 -0.0758917497
sample96   0.0024125838 -0.0470185490
sample97   0.0634545805  0.0270303528
sample98  -0.0359372560 -0.0135466362
sample99  -0.1009167606  0.1124712253
sample100  0.0551754093  0.0246502201
sample101 -0.0080116004 -0.1627407467
sample102 -0.0046451172  0.0095472047
sample103 -0.0472520874 -0.0940383468
sample104  0.0198157460 -0.0591147509
sample105 -0.0400238988 -0.0160949314
sample106 -0.0923810136  0.0369003787
sample107 -0.1019372372  0.0224967376
sample108 -0.0877091515 -0.0128849810
sample109  0.0864820282 -0.0901081721
sample110 -0.1223116477 -0.0096108628
sample111  0.0257352435 -0.0936281743
sample112 -0.0765285921  0.0270379519
sample113  0.0258799855  0.0377438101
sample114  0.0021141088 -0.0882040276
sample115  0.0303455298 -0.0723735977
sample116  0.0780504468 -0.0685162809
sample117  0.0536894074 -0.0912025960
sample118  0.0666649895 -0.0236261221
sample119  0.1021872564 -0.2325004104
sample120  0.0750216331  0.0243345489
sample121 -0.0756937880  0.0942970531
sample122 -0.0259632055  0.0731920880
sample123 -0.1037844688 -0.0369178650
sample124  0.0611205175  0.0421646707
sample125 -0.0738472619  0.0066944242
sample126  0.0972919127  0.0762699135
sample127  0.0824699434 -0.0096644709
sample128 -0.1249411519  0.0929253540
sample129 -0.0734063701 -0.0434313369
sample130 -0.0003500256 -0.0309857226
sample131  0.0930184046  0.0155970249
sample132  0.0736220609  0.0732971881
sample133 -0.0498398358 -0.0462456028
sample134  0.1644872631  0.0720047134
sample135 -0.0752295048  0.0003869840
sample136  0.0227149964 -0.0495469258
sample137  0.0564721700 -0.0288860354
sample138  0.0255986488 -0.0610930891
sample139  0.0621218779  0.0235858009
sample140 -0.0604148951 -0.0435532081
sample141  0.0246743046  0.0532630248
sample142 -0.0409563861  0.0316234065
sample143 -0.0077356388 -0.0476908899
sample144  0.0173241004 -0.0156785904
sample145  0.0485467723  0.1202737777
sample146  0.0419649973 -0.0811240742
sample147 -0.0977304655 -0.0274770984
sample148  0.0368253292  0.0803969464
sample149 -0.0072864878 -0.1533017140
sample150  0.1020825514  0.0624822759
sample151  0.0305397165 -0.0289337287
sample152 -0.0533595211 -0.0638335147
sample153 -0.0891639414  0.1799452654
sample154 -0.0727554404 -0.0834129283
sample155 -0.0880665825 -0.0220770160
sample156 -0.0276558852 -0.0326601719
sample157 -0.1155031564  0.0183635596
sample158 -0.0281506701 -0.0104911836
sample159  0.0663233781  0.0443809613
sample160 -0.0302644006  0.0404301482
sample161  0.0114712960 -0.0591083369
sample162 -0.1337090995  0.1398131403
sample163  0.1330120758  0.1688769271
sample164 -0.0150338141  0.0028375218
sample165  0.0076518841 -0.0164145907
sample166  0.0367791501  0.0630614025
sample167  0.1111989817  0.0030066479
sample168 -0.0672982975  0.0446266676
sample169 -0.0413003638  0.0224447292
> discoRes@scores$dist[[1]] ## Distinctive scores for Block 1
                      1             2
sample1   -0.0420463429  0.0867866075
sample2   -0.0820849351 -0.0410968932
sample3    0.0155965092 -0.0195186302
sample4   -0.1001342679 -0.0410776498
sample5   -0.0153479478 -0.0253257755
sample6    0.0340240556 -0.0408223367
sample7    0.0722602020  0.0002324021
sample8   -0.0457617486 -0.0370007043
sample9   -0.0086217228  0.0820184495
sample10  -0.0423630644 -0.0083917712
sample11   0.0022592712  0.0787764136
sample12   0.0322076665  0.1479823411
sample13  -0.0293968887 -0.0306742962
sample14   0.0337431762 -0.0367508341
sample15   0.0815559862  0.1275613950
sample16   0.0508334027  0.0540604350
sample17   0.0062555924  0.0041024856
sample18   0.0705601519 -0.0351053286
sample19  -0.0476784670 -0.0509595471
sample20   0.0523026071  0.0715514159
sample21  -0.0119248928 -0.0376087160
sample22   0.0724456912 -0.0095634794
sample23  -0.0992529580  0.0134298845
sample24  -0.1595263065  0.0728683950
sample25  -0.0920661625 -0.0749749355
sample26  -0.0595566565  0.0848973576
sample27   0.0826575514 -0.0086747417
sample28  -0.0384832869  0.0440972662
sample29   0.0777739746  0.1735298618
sample30   0.1229474283 -0.0819018336
sample31   0.0579752147 -0.0238646834
sample32   0.0970366216 -0.0111435041
sample33   0.1017580249 -0.0630452479
sample34   0.0637903008  0.0377936271
sample35   0.0790003054 -0.0229732391
sample36   0.1224933157 -0.1274968212
sample37   0.1798846986 -0.1673447826
sample38   0.0466392374  0.0888153256
sample39  -0.0168694588  0.0421536019
sample40   0.1756417496 -0.1526662158
sample41   0.0042467672  0.0004924609
sample42  -0.0447825926 -0.0651501422
sample43   0.0482292298 -0.0253533492
sample44  -0.1986817672 -0.0545754015
sample45  -0.0741916694  0.0054714102
sample46   0.0478860571 -0.0007080301
sample47   0.0608216127  0.0481615512
sample48  -0.1381465161  0.0578300883
sample49  -0.0530629044 -0.1405523684
sample50  -0.0173649150  0.1602386155
sample51   0.0462458422  0.0303473043
sample52   0.0279997208  0.0280387871
sample53   0.0667500805  0.0237700165
sample54   0.0121812069 -0.0521354899
sample55   0.0182392284  0.0221326651
sample56  -0.0001307981  0.0030909275
sample57   0.0316576503  0.0530190645
sample58   0.0393891482 -0.0297801760
sample59   0.1278271722 -0.0546540474
sample60   0.1486964962  0.1069141992
sample61   0.0793068481  0.0569790467
sample62   0.1172821520 -0.0149211054
sample63  -0.0028811159  0.1300524095
sample64   0.0237297451  0.1073288387
sample65  -0.0126543476  0.0589810341
sample66  -0.0468233193 -0.0771066666
sample67   0.1494285568 -0.0769877233
sample68   0.0978022397 -0.0577363708
sample69   0.0403090435  0.0156038289
sample70   0.0221596822  0.0315436661
sample71  -0.0546331884 -0.0272394982
sample72   0.1107500796 -0.0537331271
sample73   0.0906756769  0.0579957963
sample74   0.0586514158  0.0121417500
sample75   0.0390512318  0.0349278255
sample76  -0.0022939958 -0.1676560088
sample77  -0.0232101398 -0.2067300962
sample78  -0.0929808853 -0.0434928057
sample79  -0.1619382888 -0.0378102605
sample80   0.0680392314  0.1424655990
sample81  -0.0530726585 -0.0358347709
sample82   0.0266849927 -0.0577449065
sample83   0.1517241925 -0.0448569959
sample84  -0.0570943632 -0.0273808508
sample85   0.1086271825 -0.1228130326
sample86   0.0833891077 -0.0442924726
sample87   0.0022040361 -0.0943908494
sample88  -0.0078275927 -0.1140504559
sample89   0.0611006800 -0.0094589351
sample90   0.0022941376 -0.0936254863
sample91   0.0433769995  0.3205972229
sample92  -0.1815219831 -0.0334666828
sample93   0.0267653662  0.0614425830
sample94   0.0181901074  0.0605088185
sample95  -0.0720315394 -0.0013040623
sample96  -0.0559673417 -0.0118787184
sample97  -0.0217420453  0.0195417178
sample98   0.0379198903  0.0588352796
sample99  -0.0792506813 -0.0151262479
sample100  0.0222100617 -0.0023322917
sample101 -0.0387086727  0.1224225197
sample102 -0.2094625815 -0.0516421075
sample103  0.0138556644  0.0301047667
sample104 -0.0807948700 -0.0162712461
sample105 -0.0520491901 -0.1229660404
sample106 -0.0192642466 -0.0185235195
sample107  0.0319014429  0.0405120602
sample108 -0.0140674463  0.0163422326
sample109 -0.1831858192  0.0613023515
sample110 -0.0292782766 -0.0199846511
sample111 -0.1423175105  0.0327351961
sample112  0.0426313600 -0.0029087019
sample113 -0.0771931667  0.0268742653
sample114 -0.0241569160 -0.0184080657
sample115 -0.1958957080  0.0460148408
sample116 -0.1394438038 -0.0530793624
sample117 -0.1672312575 -0.1386522107
sample118 -0.0448331803 -0.0117618027
sample119 -0.0910195833  0.2217435718
sample120 -0.0331404752 -0.0057270369
sample121  0.0307517324  0.1392506210
sample122 -0.0839837077 -0.0291983714
sample123  0.0239675015 -0.0642167371
sample124 -0.0909176072  0.0130430028
sample125 -0.0065362264 -0.1092631026
sample126  0.0935273723  0.1368276904
sample127  0.0035405519  0.0292755015
sample128 -0.0660349669  0.1018575705
sample129  0.0693670807 -0.0695430182
sample130  0.0008516888 -0.0669705381
sample131  0.0431012063  0.0174061044
sample132 -0.0637088576  0.0029383432
sample133 -0.0289464886 -0.0390817320
sample134  0.0446142562  0.0456332329
sample135  0.0712343727  0.0521627666
sample136  0.0596318095  0.0197291755
sample137  0.0793175326 -0.0380637213
sample138 -0.0973505938 -0.0454210204
sample139  0.0539866374 -0.1534332064
sample140  0.0850871779  0.0955804521
sample141 -0.0192723553 -0.0554446499
sample142 -0.0672294170 -0.0461313146
sample143 -0.0303707314 -0.0519258562
sample144 -0.0089350667  0.0145815363
sample145 -0.0638876127  0.0122268646
sample146  0.0585922128  0.0063074965
sample147  0.0894146696 -0.1124625709
sample148 -0.0216439123 -0.0615962443
sample149 -0.0515317213 -0.0839902877
sample150  0.0568229155 -0.0124472700
sample151 -0.0789513798 -0.0261824012
sample152 -0.0330693746  0.1306444979
sample153 -0.1752064376  0.1497755308
sample154  0.0421489313 -0.0037017063
sample155  0.0680198671  0.0095703573
sample156  0.0388949973  0.1057557991
sample157  0.0314765128  0.0561364670
sample158  0.0329630194  0.0353943649
sample159 -0.0398461331 -0.1007368330
sample160  0.0424906002  0.0108493080
sample161 -0.0888340469 -0.0679692893
sample162 -0.0027570214  0.1237848258
sample163 -0.0126228604  0.0725440843
sample164 -0.0566787154 -0.0458318343
sample165 -0.0315331593 -0.0236359606
sample166 -0.0612108940 -0.0425224894
sample167  0.0142729562  0.0179307005
sample168 -0.0169542765 -0.0769614893
sample169  0.0675063501  0.0131499125
> discoRes@scores$dist[[2]] ## Distinctive scores for Block 2
                      1             2
sample1    0.0012331664 -1.635716e-01
sample2    0.0724353214 -6.022129e-03
sample3    0.0188459942 -1.080029e-01
sample4   -0.0390143126  3.106536e-04
sample5   -0.1774810628 -2.996429e-02
sample6    0.0451446459 -3.455898e-02
sample7    0.0226463483 -7.019211e-03
sample8    0.1033684557 -9.857947e-03
sample9   -0.1350014218  8.979114e-02
sample10  -0.1259884418 -5.097937e-02
sample11  -0.0979790924  7.086567e-02
sample12   0.0863020983 -8.620322e-02
sample13   0.1381401833  1.827998e-01
sample14   0.0615074736 -2.642808e-02
sample15  -0.0381600589 -3.101602e-02
sample16   0.0048779392  1.271024e-03
sample17   0.0788483226 -1.547606e-02
sample18   0.0884189495 -3.795477e-02
sample19  -0.0703043518 -1.084003e-01
sample20   0.0025581352  7.975970e-02
sample21  -0.0941596636 -4.126893e-02
sample22   0.0550270859 -7.806617e-02
sample23  -0.0679492816 -4.102077e-02
sample24   0.1310969448  1.649282e-01
sample25  -0.0113583563 -4.426900e-02
sample26   0.1402948912  2.016459e-02
sample27  -0.0261566049  1.589958e-03
sample28   0.0724200786  5.850510e-02
sample29   0.0330054766  2.062077e-03
sample30   0.0228750328 -2.015344e-02
sample31   0.0635070407 -6.670369e-02
sample32  -0.0685100007 -4.955246e-02
sample33   0.0777764924 -1.272070e-01
sample34  -0.0157842087 -3.024311e-02
sample35   0.0529627929  1.500981e-01
sample36  -0.0070907984  2.025321e-01
sample37   0.0442411797  1.802109e-01
sample38   0.0781508374 -3.676299e-02
sample39  -0.0120330068 -3.388883e-02
sample40   0.0473283832  1.471582e-01
sample41  -0.0228192193 -2.673458e-02
sample42   0.0245361861 -7.960878e-02
sample43  -0.1036362015 -8.229577e-02
sample44   0.1012234788  7.049241e-02
sample45  -0.0013726691 -2.451069e-02
sample46   0.0558506449  2.948581e-03
sample47   0.0380478713  4.554237e-02
sample48  -0.0784340459  4.888892e-02
sample49   0.0605168075 -1.162471e-02
sample50  -0.0530082918 -2.737814e-02
sample51  -0.1514645352  5.678260e-02
sample52  -0.1860936011  1.246711e-01
sample53   0.0064179705 -2.701060e-02
sample54  -0.0697037563 -2.308412e-02
sample55  -0.1633577706  1.366433e-02
sample56  -0.1011483996  4.682134e-02
sample57  -0.1730374405  1.609594e-01
sample58   0.0071384888 -1.666951e-02
sample59   0.0030458471  3.005375e-02
sample60  -0.0215842195  2.665887e-01
sample61  -0.1510585336  1.002384e-01
sample62   0.0925531581 -4.845728e-02
sample63   0.0596315440 -4.137108e-02
sample64   0.0449227283 -2.600959e-03
sample65  -0.0939382248 -4.406950e-02
sample66  -0.1063397735 -5.710078e-02
sample67   0.0201580809  2.361746e-01
sample68  -0.0037208393  2.418542e-02
sample69   0.0645161995 -1.155618e-01
sample70   0.1013439745 -1.351780e-01
sample71   0.0016466104 -2.976774e-02
sample72  -0.0328895410 -2.835772e-02
sample73  -0.0275080392 -5.148153e-02
sample74  -0.1341718370 -7.895303e-02
sample75  -0.0951576646 -3.943148e-02
sample76   0.0864719946  3.035053e-02
sample77   0.1035749505 -2.545325e-02
sample78   0.1575647873  4.939475e-02
sample79  -0.0189138372  4.874690e-02
sample80  -0.1384142773  4.314977e-05
sample81   0.0118846665 -6.357908e-02
sample82   0.1675306637  3.533968e-02
sample83   0.0065671150 -7.812498e-02
sample84  -0.1486890659 -3.109096e-02
sample85   0.0532720342  7.417988e-02
sample86   0.1138474913 -1.820619e-05
sample87  -0.0432865949  6.080499e-02
sample88  -0.0433451195  1.402486e-01
sample89  -0.0331204803 -1.395428e-02
sample90   0.0607413476 -8.610386e-02
sample91   0.0566263751  1.303770e-01
sample92   0.0359580702  1.061605e-01
sample93   0.0433646455 -4.443610e-02
sample94   0.0477292127 -1.059571e-01
sample95   0.0249595925 -3.980510e-02
sample96  -0.0035217581 -9.293931e-02
sample97   0.0066052001 -1.527234e-01
sample98  -0.0020367066 -5.579515e-02
sample99   0.0886621728 -3.728373e-02
sample100  0.1091259602 -3.560401e-02
sample101  0.0739723834 -4.317885e-02
sample102 -0.0574455708 -2.784085e-02
sample103 -0.0142733750  9.706349e-03
sample104 -0.0710395580  4.068331e-02
sample105 -0.0980829943 -3.452996e-02
sample106  0.0254260494  3.628933e-02
sample107  0.0160655037 -9.173398e-02
sample108  0.0200988311 -2.379699e-02
sample109  0.0389781944  1.692312e-02
sample110  0.0326305251  2.988087e-02
sample111 -0.0676935936 -6.038249e-02
sample112 -0.0167883512  5.336924e-03
sample113 -0.0969213956 -2.757703e-02
sample114  0.0026397975 -9.209102e-02
sample115  0.0308049568  1.603744e-02
sample116  0.1240306398  1.272998e-01
sample117 -0.0334728648  5.392662e-02
sample118  0.1037152160  6.252440e-02
sample119  0.1064170593  1.196217e-01
sample120  0.0771357706 -1.004935e-01
sample121  0.0129352313  3.181915e-02
sample122 -0.0847487562 -5.568463e-02
sample123  0.0041335518  7.693550e-03
sample124  0.0583462201 -8.396475e-02
sample125 -0.0634843255 -5.232567e-02
sample126  0.0662582095 -1.091730e-01
sample127  0.0865025614 -1.094172e-01
sample128  0.0627822026 -1.471093e-02
sample129  0.0336274588 -4.007775e-02
sample130  0.0293518112 -8.046087e-02
sample131  0.0469196793 -2.209386e-03
sample132  0.0241745629 -1.248608e-01
sample133 -0.0907303799  1.466698e-02
sample134  0.0350841233  7.539660e-02
sample135 -0.0001334881  9.185816e-03
sample136  0.0335874805 -9.860182e-02
sample137  0.0640147270 -7.554372e-02
sample138 -0.0060964048 -1.742782e-02
sample139  0.0592082763  5.615006e-02
sample140 -0.0427988603 -1.099466e-02
sample141 -0.0618793277 -9.301101e-02
sample142 -0.0898552510  3.573324e-02
sample143 -0.0817391061  8.880528e-02
sample144 -0.0787754475 -3.821395e-02
sample145 -0.1085819510  1.569461e-01
sample146  0.0589555004 -4.373237e-02
sample147  0.0495327913  7.278054e-03
sample148 -0.1161590489  9.078141e-03
sample149  0.0121575510  7.788462e-02
sample150  0.0314511978  3.520220e-02
sample151 -0.0575380946 -1.945392e-02
sample152  0.0494540362  7.025566e-02
sample153  0.0941338535  2.153270e-01
sample154  0.0335928833  2.078824e-02
sample155 -0.0690459045 -2.780362e-02
sample156 -0.1039902304 -6.292488e-02
sample157  0.0408645840  8.065530e-03
sample158 -0.1018106341  7.817021e-03
sample159  0.0281732526 -1.207260e-02
sample160 -0.1643052865  2.977812e-03
sample161 -0.0374330079  8.524589e-02
sample162  0.0804538262  8.349636e-02
sample163  0.0743232389 -1.406346e-02
sample164 -0.1208804283 -2.139524e-02
sample165 -0.1608115954  2.025159e-02
sample166  0.0425947928 -2.660800e-02
sample167  0.0226849506 -4.464258e-02
sample168  0.0180737364 -7.471519e-04
sample169 -0.0190780207  2.645426e-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 
 17.539   0.673  18.214 

Example timings

STATegRa.Rcheck/STATegRa-Ex.timings

nameusersystemelapsed
STATegRaUsersGuide0.0010.0000.002
STATegRa_data0.3160.0170.333
STATegRa_data_TCGA_BRCA0.0030.0020.006
bioDist0.8190.0650.885
bioDistFeature0.5350.0310.568
bioDistFeaturePlot0.4720.0250.499
bioDistW0.5240.0260.550
bioDistWPlot0.5200.0280.549
bioMap0.0050.0020.006
combiningMappings0.0210.0080.074
createOmicsExpressionSet0.2000.0040.209
getInitialData0.9890.2311.221
getLoadings0.9230.2071.130
getMethodInfo0.9490.1421.092
getPreprocessing1.3721.0892.507
getScores0.9650.1121.083
getVAF0.8510.1330.985
holistOmics0.0030.0010.005
modelSelection2.2792.4484.811
omicsCompAnalysis5.6430.2345.884
omicsNPC0.0020.0010.004
plotRes7.5480.1667.721
plotVAF6.1200.1616.290