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CHECK report for STATegRa on tokay1

This page was generated on 2019-04-13 11:24:32 -0400 (Sat, 13 Apr 2019).

Package 1516/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
STATegRa 1.18.0
David Gomez-Cabrero , NĂºria Planell
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/STATegRa
Branch: RELEASE_3_8
Last Commit: b7a1407
Last Changed Date: 2018-10-30 11:41:55 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: STATegRa
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:STATegRa.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings STATegRa_1.18.0.tar.gz
StartedAt: 2019-04-13 05:45:47 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 05:52:42 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 415.5 seconds
RetCode: 0
Status:  OK  
CheckDir: STATegRa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:STATegRa.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings STATegRa_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/STATegRa.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'STATegRa/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'STATegRa' version '1.18.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
plotRes 5.23   0.11    5.35
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'STATEgRa_Example.omicsCLUST.R'
  Running 'STATEgRa_Example.omicsPCA.R'
  Running 'STATegRa_Example.omicsNPC.R'
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/STATegRa.Rcheck/00check.log'
for details.



Installation output

STATegRa.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/STATegRa_1.18.0.tar.gz && rm -rf STATegRa.buildbin-libdir && mkdir STATegRa.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=STATegRa.buildbin-libdir STATegRa_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL STATegRa_1.18.0.zip && rm STATegRa_1.18.0.tar.gz STATegRa_1.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3179k  100 3179k    0     0  33.4M      0 --:--:-- --:--:-- --:--:-- 34.8M

install for i386

* installing *source* package 'STATegRa' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'STATegRa'
    finding HTML links ... done
    STATegRa-defunct                        html  
    STATegRa                                html  
    STATegRaUsersGuide                      html  
    STATegRa_data                           html  
    STATegRa_data_TCGA_BRCA                 html  
    bioDist                                 html  
    bioDistFeature                          html  
    bioDistFeaturePlot                      html  
    bioDistW                                html  
    bioDistWPlot                            html  
    bioDistclass                            html  
    bioMap                                  html  
    caClass-class                           html  
    combiningMappings                       html  
    createOmicsExpressionSet                html  
    getInitialData                          html  
    getLoadings                             html  
    getMethodInfo                           html  
    getPreprocessing                        html  
    getScores                               html  
    getVAF                                  html  
    holistOmics                             html  
    modelSelection                          html  
    finding level-2 HTML links ... done

    omicsCompAnalysis                       html  
    omicsNPC                                html  
    plotRes                                 html  
    plotVAF                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'STATegRa' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'STATegRa' as STATegRa_1.18.0.zip
* DONE (STATegRa)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'STATegRa' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

STATegRa.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 -- Sat Apr 13 05:50:26 2019 
*********************************************** 
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 
   3.26    0.29    3.62 

STATegRa.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Sat Apr 13 05:52:37 2019 
*********************************************** 
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 
   3.92    0.20    4.11 

STATegRa.Rcheck/tests_i386/STATEgRa_Example.omicsCLUST.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> 
> # 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
> 
> #############################################
> ## 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 
  25.17    0.92   26.09 

STATegRa.Rcheck/tests_x64/STATEgRa_Example.omicsCLUST.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> 
> # 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 
  32.67    0.76   33.42 

STATegRa.Rcheck/tests_i386/STATegRa_Example.omicsNPC.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  61.51    0.21   61.71 

STATegRa.Rcheck/tests_x64/STATegRa_Example.omicsNPC.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  80.10    0.26   80.35 

STATegRa.Rcheck/tests_i386/STATEgRa_Example.omicsPCA.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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    0.0781574324 -0.0431502484
sample2   -0.1192218439  0.0294088068
sample3   -0.0531412091 -0.0746839775
sample4    0.0292975129 -0.0005960586
sample5    0.0202091778  0.0110463549
sample6    0.1226089047  0.1053467340
sample7    0.1078928134 -0.0322475303
sample8    0.1782895256  0.1449363805
sample9    0.0468698136 -0.0455174410
sample10  -0.0036030513  0.0420110684
sample11  -0.0035566458 -0.0566292629
sample12   0.1006128899  0.0641380920
sample13  -0.1174408396  0.0907488345
sample14   0.0981203255  0.0617738383
sample15   0.0085334337 -0.0087013100
sample16   0.0783148647  0.1581294771
sample17  -0.1483609935  0.0638581974
sample18  -0.0963086248  0.0556640610
sample19  -0.0217244076 -0.0720086525
sample20  -0.0635636387 -0.0779652826
sample21  -0.0201840354  0.1566391236
sample22   0.0218268763 -0.0764103992
sample23   0.0852042003 -0.0032689424
sample24  -0.1287170737  0.1924542709
sample25  -0.0430574160 -0.0456566674
sample26  -0.1453896883  0.0541511817
sample27  -0.0197488766 -0.1185656342
sample28  -0.1025336339  0.0650685336
sample29   0.0706018514 -0.0682987702
sample30  -0.1295627496 -0.0066768577
sample31   0.1147449118  0.1232686989
sample32  -0.0374310845  0.0380178473
sample33   0.0599516020  0.0136867804
sample34  -0.0984200803  0.0375321382
sample35  -0.0543098361 -0.0378105380
sample36   0.1403625470 -0.0343755274
sample37   0.0228941924 -0.0732845086
sample38  -0.0222077237 -0.0962594572
sample39  -0.0941738496  0.0215199046
sample40   0.0643801197 -0.0687869839
sample41  -0.0327638001 -0.1232188164
sample42  -0.0500431841 -0.0292473609
sample43  -0.0184498796  0.0233011273
sample44   0.1487898698  0.1171353305
sample45  -0.1050774209  0.1123201104
sample46  -0.1151195696 -0.1094028484
sample47  -0.0962593717 -0.0288463393
sample48   0.0004837300 -0.0310278658
sample49   0.1135207753  0.1213972782
sample50  -0.0123553101 -0.1740743888
sample51   0.0550529876  0.1258886898
sample52   0.0499121236  0.0728544646
sample53   0.1119773650  0.1588014207
sample54  -0.0360055665  0.0228575635
sample55   0.0210419016  0.0006731746
sample56  -0.0434169231  0.0633126023
sample57   0.0197824614  0.1150713703
sample58   0.0030439898  0.0326098202
sample59   0.0500253148  0.0129419501
sample60   0.0184278677  0.0136086059
sample61   0.0150299434  0.0635026141
sample62  -0.0304763874 -0.0201318720
sample63   0.1102252451  0.1285976926
sample64   0.1552588073  0.0971168455
sample65  -0.0058503050  0.0207115321
sample66  -0.0025605347  0.0424319701
sample67   0.1546634851 -0.0661715689
sample68   0.0536369307 -0.0923683286
sample69   0.0640330376  0.0081983249
sample70   0.0163517751 -0.0663230005
sample71  -0.0102537625 -0.1345921601
sample72  -0.0654196012 -0.0196119114
sample73  -0.1048556118  0.0220938563
sample74   0.0123799502  0.0586115261
sample75   0.0392077960 -0.0209754955
sample76   0.0648953379 -0.0524764313
sample77   0.1172922120 -0.0201186686
sample78  -0.1463068137  0.0708472166
sample79   0.0265211179 -0.1603308514
sample80   0.0279737180 -0.0214204975
sample81   0.0079211492 -0.0738451038
sample82  -0.1544236518 -0.0361467732
sample83  -0.0494211367 -0.0050047995
sample84  -0.0259038460 -0.0346549840
sample85   0.1116484368 -0.0031497291
sample86  -0.1306483028 -0.0377214866
sample87  -0.0554778191 -0.0459748914
sample88  -0.0301623847  0.0382197572
sample89  -0.1016866706  0.0694033988
sample90   0.0086819876 -0.0201320073
sample91   0.1578625345 -0.2097827919
sample92   0.0170936809 -0.1655807425
sample93  -0.0979806820 -0.0121512179
sample94   0.0131484095 -0.0114932045
sample95   0.0315682620 -0.0758859297
sample96   0.0024125612 -0.0470135726
sample97   0.0634545408  0.0270331823
sample98  -0.0359374631 -0.0135488370
sample99  -0.1009163353  0.1124779877
sample100  0.0551753120  0.0246489670
sample101 -0.0080118900 -0.1627368617
sample102 -0.0046444334  0.0095631466
sample103 -0.0472523170 -0.0940393285
sample104  0.0198159484 -0.0591091786
sample105 -0.0400237790 -0.0160912130
sample106 -0.0923808424  0.0369017699
sample107 -0.1019373947  0.0224954209
sample108 -0.0877091657 -0.0128834228
sample109  0.0864824362 -0.0900942053
sample110 -0.1223115546 -0.0096085752
sample111  0.0257354627 -0.0936169424
sample112 -0.0765286599  0.0270347628
sample113  0.0258803241  0.0377497049
sample114  0.0021138923 -0.0882014926
sample115  0.0303460179 -0.0723585980
sample116  0.0780508400 -0.0685066495
sample117  0.0536898099 -0.0911908651
sample118  0.0666651136 -0.0236231066
sample119  0.1021871616 -0.2324936916
sample120  0.0750216541  0.0243379127
sample121 -0.0756936404  0.0942950616
sample122 -0.0259628087  0.0731987035
sample123 -0.1037846252 -0.0369197165
sample124  0.0611207907  0.0421723557
sample125 -0.0738472709  0.0066950109
sample126  0.0972916437  0.0762640151
sample127  0.0824697622 -0.0096637260
sample128 -0.1249407666  0.0929312602
sample129 -0.0734067512 -0.0434362795
sample130 -0.0003502006 -0.0309852640
sample131  0.0930182811  0.0155937212
sample132  0.0736222799  0.0733029755
sample133 -0.0498397969 -0.0462437540
sample134  0.1644873489  0.0720005686
sample135 -0.0752297195  0.0003817834
sample136  0.0227145775 -0.0495505932
sample137  0.0564717412 -0.0288915605
sample138  0.0255988105 -0.0610857142
sample139  0.0621217803  0.0235807814
sample140 -0.0604152525 -0.0435593182
sample141  0.0246743972  0.0532648650
sample142 -0.0409560326  0.0316279740
sample143 -0.0077355213 -0.0476896350
sample144  0.0173240832 -0.0156777990
sample145  0.0485474521  0.1202770469
sample146  0.0419645634 -0.0811281193
sample147 -0.0977308346 -0.0274839894
sample148  0.0368256194  0.0803979600
sample149 -0.0072865791 -0.1532986055
sample150  0.1020825288  0.0624774724
sample151  0.0305399064 -0.0289278313
sample152 -0.0533594807 -0.0638309150
sample153 -0.0891627687  0.1799578145
sample154 -0.0727557469 -0.0834160836
sample155 -0.0880668551 -0.0220819531
sample156 -0.0276561035 -0.0326625329
sample157 -0.1155032192  0.0183616134
sample158 -0.0281507508 -0.0104938649
sample159  0.0663235703  0.0443837319
sample160 -0.0302643870  0.0404265452
sample161  0.0114715566 -0.0591025580
sample162 -0.1337087140  0.1398135497
sample163  0.1330124463  0.1688781288
sample164 -0.0150336087  0.0028416064
sample165  0.0076520288 -0.0164128501
sample166  0.0367794360  0.0630661997
sample167  0.1111988864  0.0030057884
sample168 -0.0672981605  0.0446279312
sample169 -0.0413004965  0.0224394347
> discoRes@scores$dist[[1]] ## Distinctive scores for Block 1
                     1             2
sample1    0.042051465  0.0867863099
sample2    0.082082866 -0.0410977991
sample3   -0.015589993 -0.0195182400
sample4    0.100133713 -0.0410786631
sample5    0.015346598 -0.0253259666
sample6   -0.034032563 -0.0408223188
sample7   -0.072257981  0.0002332197
sample8    0.045750024 -0.0370016169
sample9    0.008624917  0.0820184905
sample10   0.042359867 -0.0083923249
sample11  -0.002254875  0.0787766035
sample12  -0.032210574  0.1479824683
sample13   0.029388998 -0.0306748589
sample14  -0.033748255 -0.0367506861
sample15  -0.081553919  0.1275622451
sample16  -0.050845197  0.0540604669
sample17  -0.006259661  0.0041023722
sample18  -0.070563973 -0.0351047716
sample19   0.047684160 -0.0509598082
sample20  -0.052296296  0.0715521820
sample21   0.011912692 -0.0376093046
sample22  -0.072439322 -0.0095625169
sample23   0.099253214  0.0134288839
sample24   0.159511839  0.0728662133
sample25   0.092069333 -0.0749757236
sample26   0.059554016  0.0848966074
sample27  -0.082648582 -0.0086735490
sample28   0.038478827  0.0440966904
sample29  -0.077767168  0.1735308466
sample30  -0.122947127 -0.0819005581
sample31  -0.057984619 -0.0238644754
sample32  -0.097039313 -0.0111426333
sample33  -0.101758796 -0.0630442614
sample34  -0.063792284  0.0377941689
sample35  -0.078998449 -0.0229723262
sample36  -0.122493928 -0.1274954993
sample37  -0.179882079 -0.1673427518
sample38  -0.046630463  0.0888160900
sample39   0.016868765  0.0421533765
sample40  -0.175639211 -0.1526642442
sample41  -0.004237093  0.0004928773
sample42   0.044784970 -0.0651504997
sample43  -0.048230841 -0.0253529286
sample44   0.198671494 -0.0545777759
sample45   0.074183654  0.0054703336
sample46  -0.047877223 -0.0007072066
sample47  -0.060818856  0.0481622604
sample48   0.138148936  0.0578287829
sample49   0.053052059 -0.1405532786
sample50   0.017379962  0.1602389639
sample51  -0.046256096  0.0303473853
sample52  -0.028006502  0.0280388409
sample53  -0.066762131  0.0237702050
sample54  -0.012183354 -0.0521354321
sample55  -0.018239595  0.0221328433
sample56   0.000125558  0.0030907376
sample57  -0.031667545  0.0530190304
sample58  -0.039391814 -0.0297798755
sample59  -0.127829089 -0.0546527999
sample60  -0.148698514  0.1069156510
sample61  -0.079312251  0.0569796515
sample62  -0.117280101 -0.0149198544
sample63   0.002872680  0.1300519861
sample64  -0.023736466  0.1073287732
sample65   0.012653488  0.0589808449
sample66   0.046819481 -0.0771072663
sample67  -0.149426458 -0.0769860359
sample68  -0.097796121 -0.0577351109
sample69  -0.040308729  0.0156042100
sample70  -0.022153128  0.0315440929
sample71   0.054643457 -0.0272396445
sample72  -0.110748779 -0.0537319424
sample73  -0.090676127  0.0579966573
sample74  -0.058655541  0.0121421666
sample75  -0.039049330  0.0349282797
sample76   0.002296077 -0.1676558804
sample77   0.023209630 -0.2067302793
sample78   0.092975500 -0.0434939444
sample79   0.161949679 -0.0378114200
sample80  -0.068036559  0.1424663468
sample81   0.053078408 -0.0358350842
sample82  -0.026682192 -0.0577445133
sample83  -0.151723518 -0.0448554404
sample84   0.057096710 -0.0273813220
sample85  -0.108628966 -0.1228119373
sample86  -0.083385991 -0.0442915033
sample87  -0.002201839 -0.0943906864
sample88   0.007822492 -0.1140506517
sample89  -0.061105726 -0.0094585165
sample90  -0.002292806 -0.0936254001
sample91  -0.043359058  0.3205982730
sample92   0.181533554 -0.0334680247
sample93  -0.026763076  0.0614429008
sample94  -0.018187777  0.0605090394
sample95   0.072037573 -0.0013045639
sample96   0.055971479 -0.0118791403
sample97   0.021741102  0.0195414158
sample98  -0.037917740  0.0588357085
sample99   0.079242730 -0.0151273750
sample100 -0.022211640 -0.0023321441
sample101  0.038722860  0.1224226199
sample102  0.209461417 -0.0516442524
sample103 -0.013848122  0.0301051929
sample104  0.080798702 -0.0162718890
sample105  0.052049337 -0.1229665144
sample106  0.019261330 -0.0185238172
sample107 -0.031901716  0.0405123275
sample108  0.014069100  0.0163421382
sample109  0.183193012  0.0613007625
sample110  0.029279061 -0.0199849074
sample111  0.142325203  0.0327340375
sample112 -0.042633286 -0.0029083455
sample113  0.077190451  0.0268733693
sample114  0.024164145 -0.0184080424
sample115  0.195901560  0.0460130753
sample116  0.139447603 -0.0530805758
sample117  0.167236184 -0.1386536341
sample118  0.044834430 -0.0117621919
sample119  0.091038634  0.2217433378
sample120  0.033139224 -0.0057274479
sample121 -0.030757492  0.1392506548
sample122  0.083978116 -0.0291994367
sample123 -0.023965039 -0.0642163747
sample124  0.090915064  0.0130419549
sample125  0.006535088 -0.1092631810
sample126 -0.093531186  0.1368284018
sample127 -0.003538788  0.0292755630
sample128  0.066029546  0.1018566369
sample129 -0.069363856 -0.0695421784
sample130 -0.000849341 -0.0669704337
sample131 -0.043102401  0.0174064851
sample132  0.063704013  0.0029374766
sample133  0.028949477 -0.0390818825
sample134 -0.044620303  0.0456334505
sample135 -0.071233699  0.0521634920
sample136 -0.059627099  0.0197299282
sample137 -0.079315194 -0.0380628351
sample138  0.097354836 -0.0454218228
sample139 -0.053990468 -0.1534327384
sample140 -0.085082703  0.0955814482
sample141  0.019268183 -0.0554450046
sample142  0.067226201 -0.0461320873
sample143  0.030373043 -0.0519260229
sample144  0.008936457  0.0145814918
sample145  0.063876991  0.0122258474
sample146 -0.058585630  0.0063083303
sample147 -0.089413330 -0.1124615754
sample148  0.021636695 -0.0615967093
sample149  0.051542074 -0.0839903500
sample150 -0.056828334 -0.0124468934
sample151  0.078953240 -0.0261831151
sample152  0.033075346  0.1306443586
sample153  0.175193122  0.1497732225
sample154 -0.042142432 -0.0037010235
sample155 -0.068017751  0.0095711192
sample156 -0.038891118  0.1057562936
sample157 -0.031476942  0.0561367409
sample158 -0.032962057  0.0353947308
sample159  0.039841660 -0.1007373744
sample160 -0.042493878  0.0108496170
sample161  0.088837133 -0.0679700137
sample162  0.002747589  0.1237843889
sample163  0.012610524  0.0725434388
sample164  0.056677966 -0.0458324149
sample165  0.031533638 -0.0236362331
sample166  0.061205815 -0.0425232995
sample167 -0.014272987  0.0179308270
sample168  0.016950351 -0.0769617882
sample169 -0.067508036  0.0131505302
> discoRes@scores$dist[[2]] ## Distinctive scores for Block 2
                      1             2
sample1   -0.0012329671 -1.635717e-01
sample2   -0.0724350068 -6.021270e-03
sample3   -0.0188460444 -1.080036e-01
sample4    0.0390145267  3.114055e-04
sample5    0.1774811636 -2.996385e-02
sample6   -0.0451444415 -3.455859e-02
sample7   -0.0226466248 -7.020151e-03
sample8   -0.1033680239 -9.856798e-03
sample9    0.1350011726  8.979099e-02
sample10   0.1259887248 -5.097853e-02
sample11   0.0979788360  7.086535e-02
sample12  -0.0863019103 -8.620317e-02
sample13  -0.1381401102  1.828007e-01
sample14  -0.0615073855 -2.642803e-02
sample15   0.0381598958 -3.101663e-02
sample16  -0.0048776715  1.271833e-03
sample17  -0.0788480934 -1.547554e-02
sample18  -0.0884188733 -3.795487e-02
sample19   0.0703044409 -1.084004e-01
sample20  -0.0025585524  7.975876e-02
sample21   0.0941601677 -4.126742e-02
sample22  -0.0550273412 -7.806742e-02
sample23   0.0679495287 -4.102006e-02
sample24  -0.1310962794  1.649309e-01
sample25   0.0113585267 -4.426863e-02
sample26  -0.1402945914  2.016542e-02
sample27   0.0261561128  1.588460e-03
sample28  -0.0724198713  5.850591e-02
sample29  -0.0330058579  2.060838e-03
sample30  -0.0228752531 -2.015429e-02
sample31  -0.0635067929 -6.670334e-02
sample32   0.0685099670 -4.955272e-02
sample33  -0.0777765202 -1.272078e-01
sample34   0.0157842430 -3.024314e-02
sample35  -0.0529632752  1.500972e-01
sample36   0.0070900768  2.025307e-01
sample37  -0.0442420577  1.802089e-01
sample38  -0.0781511305 -3.676419e-02
sample39   0.0120331862 -3.388842e-02
sample40  -0.0473292054  1.471562e-01
sample41   0.0228189398 -2.673554e-02
sample42  -0.0245360247 -7.960867e-02
sample43   0.1036362820 -8.229577e-02
sample44  -0.1012228820  7.049449e-02
sample45   0.0013732050 -2.450912e-02
sample46  -0.0558510017  2.947394e-03
sample47  -0.0380481171  4.554174e-02
sample48   0.0784342059  4.888980e-02
sample49  -0.0605163956 -1.162356e-02
sample50   0.0530079240 -2.737931e-02
sample51   0.1514646546  5.678344e-02
sample52   0.1860935241  1.246717e-01
sample53  -0.0064177076 -2.700994e-02
sample54   0.0697038352 -2.308389e-02
sample55   0.1633577033  1.366442e-02
sample56   0.1011485110  4.682205e-02
sample57   0.1730374224  1.609603e-01
sample58  -0.0071384697 -1.666955e-02
sample59  -0.0030461667  3.005286e-02
sample60   0.0215835148  2.665878e-01
sample61   0.1510583651  1.002385e-01
sample62  -0.0925533935 -4.845841e-02
sample63  -0.0596311787 -4.137023e-02
sample64  -0.0449225798 -2.600585e-03
sample65   0.0939383760 -4.406909e-02
sample66   0.1063400756 -5.709993e-02
sample67  -0.0201590014  2.361728e-01
sample68   0.0037203204  2.418391e-02
sample69  -0.0645161202 -1.155622e-01
sample70  -0.1013440019 -1.351789e-01
sample71  -0.0016467899 -2.976841e-02
sample72   0.0328893040 -2.835856e-02
sample73   0.0275080064 -5.148185e-02
sample74   0.1341719702 -7.895280e-02
sample75   0.0951575663 -3.943183e-02
sample76  -0.0864721969  3.034992e-02
sample77  -0.1035749570 -2.545353e-02
sample78  -0.1575644128  4.939593e-02
sample79   0.0189137036  4.874679e-02
sample80   0.1384140584  4.266004e-05
sample81  -0.0118846472 -6.357931e-02
sample82  -0.1675308160  3.533912e-02
sample83  -0.0065673383 -7.812608e-02
sample84   0.1486891604 -3.109057e-02
sample85  -0.0532724411  7.417885e-02
sample86  -0.1138477321 -1.914675e-05
sample87   0.0432863984  6.080473e-02
sample88   0.0433450375  1.402491e-01
sample89   0.0331205803 -1.395401e-02
sample90  -0.0607412811 -8.610414e-02
sample91  -0.0566272688  1.303747e-01
sample92  -0.0359582552  1.061604e-01
sample93  -0.0433646356 -4.443635e-02
sample94  -0.0477291301 -1.059574e-01
sample95  -0.0249595792 -3.980525e-02
sample96   0.0035218999 -9.293928e-02
sample97  -0.0066048753 -1.527231e-01
sample98   0.0020366820 -5.579550e-02
sample99  -0.0886616077 -3.728227e-02
sample100 -0.1091259131 -3.560420e-02
sample101 -0.0739726516 -4.317998e-02
sample102  0.0574461135 -2.783915e-02
sample103  0.0142731011  9.705565e-03
sample104  0.0710395191  4.068351e-02
sample105  0.0980831350 -3.452953e-02
sample106 -0.0254259303  3.628983e-02
sample107 -0.0160653433 -9.173394e-02
sample108 -0.0200987654 -2.379692e-02
sample109 -0.0389780698  1.692358e-02
sample110 -0.0326304843  2.988109e-02
sample111  0.0676937533 -6.038213e-02
sample112  0.0167883447  5.336939e-03
sample113  0.0969217012 -2.757604e-02
sample114 -0.0026398365 -9.209156e-02
sample115 -0.0308047356  1.603822e-02
sample116 -0.1240307208  1.273000e-01
sample117  0.0334729049  5.392710e-02
sample118 -0.1037152933  6.252430e-02
sample119 -0.1064176723  1.196202e-01
sample120 -0.0771355093 -1.004933e-01
sample121 -0.0129350737  3.181975e-02
sample122  0.0847492298 -5.568327e-02
sample123 -0.0041336771  7.693184e-03
sample124 -0.0583458006 -8.396390e-02
sample125  0.0634844613 -5.232540e-02
sample126 -0.0662580936 -1.091733e-01
sample127 -0.0865024610 -1.094176e-01
sample128 -0.0627817422 -1.470965e-02
sample129 -0.0336276440 -4.007858e-02
sample130 -0.0293517746 -8.046117e-02
sample131 -0.0469197666 -2.209748e-03
sample132 -0.0241740675 -1.248598e-01
sample133  0.0907303206  1.466701e-02
sample134 -0.0350842080  7.539662e-02
sample135  0.0001333416  9.185383e-03
sample136 -0.0335876060 -9.860273e-02
sample137 -0.0640148905 -7.554469e-02
sample138  0.0060964824 -1.742762e-02
sample139 -0.0592084451  5.614969e-02
sample140  0.0427985929 -1.099550e-02
sample141  0.0618796395 -9.301038e-02
sample142  0.0898554470  3.573417e-02
sample143  0.0817389204  8.880524e-02
sample144  0.0787754778 -3.821391e-02
sample145  0.1085821583  1.569476e-01
sample146 -0.0589557949 -4.373359e-02
sample147 -0.0495330425  7.277209e-03
sample148  0.1161592802  9.079077e-03
sample149 -0.0121579485  7.788375e-02
sample150 -0.0314512532  3.520212e-02
sample151  0.0575382159 -1.945353e-02
sample152 -0.0494542118  7.025537e-02
sample153 -0.0941332737  2.153297e-01
sample154 -0.0335932013  2.078729e-02
sample155  0.0690457659 -2.780409e-02
sample156  0.1039901619 -6.292524e-02
sample157 -0.0408645772  8.065515e-03
sample158  0.1018105309  7.816879e-03
sample159 -0.0281730535 -1.207207e-02
sample160  0.1643053022  2.978106e-03
sample161  0.0374329232  8.524610e-02
sample162 -0.0804535300  8.349753e-02
sample163 -0.0743227960 -1.406226e-02
sample164  0.1208806011 -2.139460e-02
sample165  0.1608115909  2.025192e-02
sample166 -0.0425944635 -2.660715e-02
sample167 -0.0226849486 -4.464282e-02
sample168 -0.0180735569 -7.466242e-04
sample169  0.0190779017  2.645403e-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 
  11.40    0.29   11.68 

STATegRa.Rcheck/tests_x64/STATEgRa_Example.omicsPCA.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.

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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    0.0781575595  0.0431547773
sample2   -0.1192221304 -0.0294022966
sample3   -0.0531408766  0.0746837648
sample4    0.0292971865  0.0006032708
sample5    0.0202090774 -0.0110455403
sample6    0.1226088461 -0.1053492734
sample7    0.1078931262  0.0322420056
sample8    0.1782891240 -0.1449330994
sample9    0.0468697308  0.0455171750
sample10  -0.0036032635 -0.0420078340
sample11  -0.0035566367  0.0566285235
sample12   0.1006129662 -0.0641393833
sample13  -0.1174412703 -0.0907475625
sample14   0.0981203551 -0.0617763150
sample15   0.0085337190  0.0086957068
sample16   0.0783146862 -0.1581332884
sample17  -0.1483610648 -0.0638580160
sample18  -0.0963084439 -0.0556687175
sample19  -0.0217243096  0.0720127937
sample20  -0.0635633992  0.0779610894
sample21  -0.0201843907 -0.1566382141
sample22   0.0218273722  0.0764056572
sample23   0.0852039117  0.0032763817
sample24  -0.1287181247 -0.1924428066
sample25  -0.0430575606  0.0456637518
sample26  -0.1453899714 -0.0541459665
sample27  -0.0197483737  0.1185593833
sample28  -0.1025339350 -0.0650655821
sample29   0.0706022364  0.0682933746
sample30  -0.1295623088  0.0066679048
sample31   0.1147449307 -0.1232726649
sample32  -0.0374308275 -0.0380248502
sample33   0.0599520656 -0.0136935094
sample34  -0.0984199341 -0.0375363968
sample35  -0.0543096465  0.0378036237
sample36   0.1403627986  0.0343640713
sample37   0.0228947542  0.0732691952
sample38  -0.0222073126  0.0962567624
sample39  -0.0941739202 -0.0215180822
sample40   0.0643806939  0.0687722116
sample41  -0.0327635048  0.1232187221
sample42  -0.0500431637  0.0292513190
sample43  -0.0184497219 -0.0233043896
sample44   0.1487889568 -0.1171212282
sample45  -0.1050778686 -0.1123141277
sample46  -0.1151191694  0.1093996250
sample47  -0.0962591578  0.0288418693
sample48   0.0004832724  0.0310377913
sample49   0.1135203965 -0.1213937121
sample50  -0.0123549998  0.1740762654
sample51   0.0550527497 -0.1258930148
sample52   0.0499118552 -0.0728580428
sample53   0.1119772691 -0.1588063570
sample54  -0.0360055715 -0.0228585482
sample55   0.0210418834 -0.0006750450
sample56  -0.0434171443 -0.0633131191
sample57   0.0197820783 -0.1150753380
sample58   0.0030440686 -0.0326127134
sample59   0.0500256659 -0.0129520155
sample60   0.0184280055 -0.0136216204
sample61   0.0150298935 -0.0635095926
sample62  -0.0304758869  0.0201237307
sample63   0.1102250175 -0.1285968514
sample64   0.1552586858 -0.0971185016
sample65  -0.0058503800 -0.0207102922
sample66  -0.0025607422 -0.0424285069
sample67   0.1546638584  0.0661580185
sample68   0.0536374141  0.0923605237
sample69   0.0640332938 -0.0082003572
sample70   0.0163521646  0.0663227237
sample71  -0.0102536152  0.1345964315
sample72  -0.0654191850  0.0196037405
sample73  -0.1048553309 -0.0220999174
sample74   0.0123800482 -0.0586156287
sample75   0.0392079698  0.0209726587
sample76   0.0648954548  0.0524759561
sample77   0.1172922637  0.0201200172
sample78  -0.1463072520 -0.0708400595
sample79   0.0265208888  0.1603423763
sample80   0.0279739172  0.0214154078
sample81   0.0079212135  0.0738494870
sample82  -0.1544234642  0.0361450832
sample83  -0.0494205549  0.0049940461
sample84  -0.0259039702  0.0346590984
sample85   0.1116487376  0.0031405515
sample86  -0.1306479143  0.0377156818
sample87  -0.0554777870  0.0459739778
sample88  -0.0301626467 -0.0382206576
sample89  -0.1016866200 -0.0694077604
sample90   0.0086821602  0.0201323766
sample91   0.1578629675  0.2097792670
sample92   0.0170933581  0.1655934541
sample93  -0.0979805138  0.0121500628
sample94   0.0131486171  0.0114929492
sample95   0.0315682464  0.0758916295
sample96   0.0024125835  0.0470184464
sample97   0.0634545798 -0.0270304113
sample98  -0.0359372602  0.0135466812
sample99  -0.1009167518 -0.1124713647
sample100  0.0551754073 -0.0246501943
sample101 -0.0080116060  0.1627406652
sample102 -0.0046451030 -0.0095475335
sample103 -0.0472520920  0.0940383668
sample104  0.0198157502  0.0591146359
sample105 -0.0400238963  0.0160948559
sample106 -0.0923810101 -0.0369004072
sample107 -0.1019372404 -0.0224967106
sample108 -0.0877091517  0.0128849487
sample109  0.0864820369  0.0901078828
sample110 -0.1223116458  0.0096108158
sample111  0.0257352483  0.0936279419
sample112 -0.0765285936 -0.0270378859
sample113  0.0258799925 -0.0377439322
sample114  0.0021141045  0.0882039755
sample115  0.0303455401  0.0723732873
sample116  0.0780504550  0.0685160823
sample117  0.0536894158  0.0912023550
sample118  0.0666649921  0.0236260598
sample119  0.1021872550  0.2325002690
sample120  0.0750216337 -0.0243346183
sample121 -0.0756937850 -0.0942970134
sample122 -0.0259631973 -0.0731922243
sample123 -0.1037844721  0.0369179040
sample124  0.0611205232 -0.0421648296
sample125 -0.0738472622 -0.0066944351
sample126  0.0972919072 -0.0762697931
sample127  0.0824699398  0.0096644552
sample128 -0.1249411438 -0.0929254770
sample129 -0.0734063781  0.0434314398
sample130 -0.0003500292  0.0309857139
sample131  0.0930184020 -0.0155969570
sample132  0.0736220655 -0.0732973077
sample133 -0.0498398350  0.0462455650
sample134  0.1644872647 -0.0720046285
sample135 -0.0752295092 -0.0003868770
sample136  0.0227149878  0.0495470014
sample137  0.0564721612  0.0288861500
sample138  0.0255986522  0.0610929372
sample139  0.0621218756 -0.0235856958
sample140 -0.0604149024  0.0435533334
sample141  0.0246743065 -0.0532630622
sample142 -0.0409563788 -0.0316235004
sample143 -0.0077356364  0.0476908644
sample144  0.0173241001  0.0156785739
sample145  0.0485467862 -0.1202738456
sample146  0.0419649884  0.0811241577
sample147 -0.0977304733  0.0274772420
sample148  0.0368253350 -0.0803969667
sample149 -0.0072864896  0.1533016506
sample150  0.1020825508 -0.0624821767
sample151  0.0305397205  0.0289336071
sample152 -0.0533595201  0.0638334596
sample153 -0.0891639173 -0.1799455263
sample154 -0.0727554467  0.0834129936
sample155 -0.0880665882  0.0220771181
sample156 -0.0276558896  0.0326602197
sample157 -0.1155031577 -0.0183635198
sample158 -0.0281506718  0.0104912387
sample159  0.0663233820 -0.0443810175
sample160 -0.0302644004 -0.0404300739
sample161  0.0114713014  0.0591082181
sample162 -0.1337090916 -0.1398131500
sample163  0.1330120833 -0.1688769528
sample164 -0.0150338099 -0.0028376057
sample165  0.0076518870  0.0164145550
sample166  0.0367791559 -0.0630615012
sample167  0.1111989798 -0.0030066304
sample168 -0.0672982947 -0.0446266929
sample169 -0.0413003666 -0.0224446199
> discoRes@scores$dist[[1]] ## Distinctive scores for Block 1
                      1             2
sample1    0.0420464496  0.0867866014
sample2    0.0820848920 -0.0410969130
sample3   -0.0155963748 -0.0195186210
sample4    0.1001342559 -0.0410776719
sample5    0.0153479196 -0.0253257798
sample6   -0.0340242319 -0.0408223371
sample7   -0.0722601562  0.0002324201
sample8    0.0457615058 -0.0370007253
sample9    0.0086217898  0.0820184506
sample10   0.0423629982 -0.0083917836
sample11  -0.0022591794  0.0787764180
sample12  -0.0322077250  0.1479823435
sample13   0.0293967255 -0.0306743091
sample14  -0.0337432816 -0.0367508313
sample15  -0.0815559420  0.1275614136
sample16  -0.0508336457  0.0540604346
sample17  -0.0062556763  0.0041024829
sample18  -0.0705602312 -0.0351053167
sample19   0.0476785840 -0.0509595522
sample20  -0.0523024758  0.0715514331
sample21   0.0119246402 -0.0376087299
sample22  -0.0724455598 -0.0095634578
sample23   0.0992529634  0.0134298626
sample24   0.1595260087  0.0728683461
sample25   0.0920662272 -0.0749749522
sample26   0.0595566031  0.0848973410
sample27  -0.0826573662 -0.0086747149
sample28   0.0384831954  0.0440972532
sample29  -0.0777738320  0.1735298837
sample30  -0.1229474230 -0.0819018056
sample31  -0.0579754094 -0.0238646797
sample32  -0.0970366773 -0.0111434854
sample33  -0.1017580417 -0.0630452264
sample34  -0.0637903413  0.0377936387
sample35  -0.0790002672 -0.0229732190
sample36  -0.1224933298 -0.1274967925
sample37  -0.1798846464 -0.1673447380
sample38  -0.0466390551  0.0888153431
sample39   0.0168694450  0.0421535970
sample40  -0.1756416990 -0.1526661725
sample41  -0.0042465673  0.0004924709
sample42   0.0447826409 -0.0651501497
sample43  -0.0482292634 -0.0253533401
sample44   0.1986815543 -0.0545754543
sample45   0.0741915040  0.0054713860
sample46  -0.0478858745 -0.0007080113
sample47  -0.0608215551  0.0481615669
sample48   0.1381465668  0.0578300599
sample49   0.0530626786 -0.1405523892
sample50   0.0173652277  0.1602386243
sample51  -0.0462460537  0.0303473050
sample52  -0.0279998606  0.0280387875
sample53  -0.0667503293  0.0237700195
sample54  -0.0121812519 -0.0521354888
sample55  -0.0182392357  0.0221326689
sample56   0.0001306899  0.0030909228
sample57  -0.0316578540  0.0530190627
sample58  -0.0393892036 -0.0297801697
sample59  -0.1278272125 -0.0546540204
sample60  -0.1486965366  0.1069142304
sample61  -0.0793069590  0.0569790593
sample62  -0.1172821098 -0.0149210778
sample63   0.0028809431  0.1300523994
sample64  -0.0237298829  0.1073288365
sample65   0.0126543305  0.0589810298
sample66   0.0468232391 -0.0771066799
sample67  -0.1494285143 -0.0769876865
sample68  -0.0978021140 -0.0577363428
sample69  -0.0403090369  0.0156038372
sample70  -0.0221595465  0.0315436760
sample71   0.0546334003 -0.0272395004
sample72  -0.1107500533 -0.0537331010
sample73  -0.0906756855  0.0579958150
sample74  -0.0586515010  0.0121417587
sample75  -0.0390511921  0.0349278355
sample76   0.0022940368 -0.1676560057
sample77   0.0232101268 -0.2067301001
sample78   0.0929807737 -0.0434928309
sample79   0.1619385237 -0.0378102848
sample80  -0.0680391745  0.1424656154
sample81   0.0530727768 -0.0358347771
sample82  -0.0266849353 -0.0577448975
sample83  -0.1517241791 -0.0448569618
sample84   0.0570944113 -0.0273808608
sample85  -0.1086272208 -0.1228130088
sample86  -0.0833890437 -0.0442924510
sample87  -0.0022039917 -0.0943908456
sample88   0.0078274861 -0.1140504606
sample89  -0.0611007843 -0.0094589264
sample90  -0.0022941112 -0.0936254841
sample91  -0.0433766251  0.3205972470
sample92   0.1815222218 -0.0334667110
sample93  -0.0267653181  0.0614425901
sample94  -0.0181900586  0.0605088236
sample95   0.0720316640 -0.0013040727
sample96   0.0559674270 -0.0118787272
sample97   0.0217420259  0.0195417111
sample98  -0.0379198452  0.0588352892
sample99   0.0792505169 -0.0151262731
sample100 -0.0222100944 -0.0023322886
sample101  0.0387089672  0.1224225231
sample102  0.2094625569 -0.0516421543
sample103 -0.0138555082  0.0301047766
sample104  0.0807949490 -0.0162712598
sample105  0.0520491917 -0.1229660506
sample106  0.0192641862 -0.0185235262
sample107 -0.0319014480  0.0405120661
sample108  0.0140674807  0.0163422308
sample109  0.1831859684  0.0613023174
sample110  0.0292782927 -0.0199846565
sample111  0.1423176698  0.0327351715
sample112 -0.0426313998 -0.0029086943
sample113  0.0771931108  0.0268742455
sample114  0.0241570651 -0.0184080645
sample115  0.1958958294  0.0460148028
sample116  0.1394438817 -0.0530793886
sample117  0.1672313577 -0.1386522413
sample118  0.0448332060 -0.0117618111
sample119  0.0910199795  0.2217435681
sample120  0.0331404492 -0.0057270459
sample121 -0.0307518497  0.1392506211
sample122  0.0839835919 -0.0291983950
sample123 -0.0239674513 -0.0642167289
sample124  0.0909175548  0.0130429797
sample125  0.0065362017 -0.1092631043
sample126 -0.0935274497  0.1368277055
sample127 -0.0035405153  0.0292755030
sample128  0.0660348562  0.1018575497
sample129 -0.0693670149 -0.0695429995
sample130 -0.0008516412 -0.0669705356
sample131 -0.0431012308  0.0174061125
sample132  0.0637087574  0.0029383239
sample133  0.0289465499 -0.0390817349
sample134 -0.0446143806  0.0456332369
sample135 -0.0712343581  0.0521627825
sample136 -0.0596317120  0.0197291924
sample137 -0.0793174848 -0.0380637017
sample138  0.0973506808 -0.0454210375
sample139 -0.0539867183 -0.1534331964
sample140 -0.0850870844  0.0955804742
sample141  0.0192722684 -0.0554446579
sample142  0.0672293500 -0.0461313317
sample143  0.0303707786 -0.0519258597
sample144  0.0089350956  0.0145815355
sample145  0.0638873935  0.0122268413
sample146 -0.0585920768  0.0063075152
sample147 -0.0894146432 -0.1124625489
sample148  0.0216437624 -0.0615962551
sample149  0.0515319342 -0.0839902881
sample150 -0.0568230277 -0.0124472623
sample151  0.0789514179 -0.0261824166
sample152  0.0330694996  0.1306444953
sample153  0.1752061645  0.1497754791
sample154 -0.0421487970 -0.0037016908
sample155 -0.0680198232  0.0095703741
sample156 -0.0388949160  0.1057558102
sample157 -0.0314765209  0.0561364730
sample158 -0.0329629991  0.0353943729
sample159  0.0398460395 -0.1007368452
sample160 -0.0424906677  0.0108493144
sample161  0.0888341099 -0.0679693048
sample162  0.0027568282  0.1237848154
sample163  0.0126226063  0.0725440690
sample164  0.0566786994 -0.0458318470
sample165  0.0315331689 -0.0236359665
sample166  0.0612107886 -0.0425225075
sample167 -0.0142729568  0.0179307032
sample168  0.0169541945 -0.0769614961
sample169 -0.0675063847  0.0131499259
> discoRes@scores$dist[[2]] ## Distinctive scores for Block 2
                      1             2
sample1   -0.0012331622  1.635716e-01
sample2   -0.0724353149  6.022111e-03
sample3   -0.0188459952  1.080029e-01
sample4    0.0390143170 -3.106691e-04
sample5    0.1774810649  2.996428e-02
sample6   -0.0451446417  3.455897e-02
sample7   -0.0226463540  7.019231e-03
sample8   -0.1033684468  9.857923e-03
sample9    0.1350014166 -8.979113e-02
sample10   0.1259884477  5.097935e-02
sample11   0.0979790871 -7.086566e-02
sample12  -0.0863020943  8.620322e-02
sample13  -0.1381401818 -1.827998e-01
sample14  -0.0615074718  2.642808e-02
sample15   0.0381600556  3.101603e-02
sample16  -0.0048779336 -1.271041e-03
sample17  -0.0788483178  1.547605e-02
sample18  -0.0884189479  3.795477e-02
sample19   0.0703043536  1.084003e-01
sample20  -0.0025581438 -7.975968e-02
sample21   0.0941596740  4.126890e-02
sample22  -0.0550270912  7.806620e-02
sample23   0.0679492867  4.102075e-02
sample24  -0.1310969311 -1.649283e-01
sample25   0.0113583598  4.426899e-02
sample26  -0.1402948850 -2.016461e-02
sample27   0.0261565948 -1.589927e-03
sample28  -0.0724200744 -5.850512e-02
sample29  -0.0330054844 -2.062052e-03
sample30  -0.0228750374  2.015346e-02
sample31  -0.0635070356  6.670368e-02
sample32   0.0685100000  4.955247e-02
sample33  -0.0777764930  1.272070e-01
sample34   0.0157842094  3.024311e-02
sample35  -0.0529628030 -1.500981e-01
sample36   0.0070907834 -2.025320e-01
sample37  -0.0442411980 -1.802109e-01
sample38  -0.0781508434  3.676301e-02
sample39   0.0120330105  3.388883e-02
sample40  -0.0473284003 -1.471581e-01
sample41   0.0228192135  2.673460e-02
sample42  -0.0245361828  7.960877e-02
sample43   0.1036362031  8.229577e-02
sample44  -0.1012234665 -7.049245e-02
sample45   0.0013726802  2.451066e-02
sample46  -0.0558506523 -2.948556e-03
sample47  -0.0380478764 -4.554235e-02
sample48   0.0784340492 -4.888894e-02
sample49  -0.0605167990  1.162469e-02
sample50   0.0530082842  2.737816e-02
sample51   0.1514645377 -5.678262e-02
sample52   0.1860935995 -1.246711e-01
sample53  -0.0064179651  2.701058e-02
sample54   0.0697037579  2.308412e-02
sample55   0.1633577692 -1.366433e-02
sample56   0.1011484019 -4.682135e-02
sample57   0.1730374401 -1.609594e-01
sample58  -0.0071384884  1.666951e-02
sample59  -0.0030458537 -3.005374e-02
sample60   0.0215842049 -2.665887e-01
sample61   0.1510585301 -1.002384e-01
sample62  -0.0925531630  4.845731e-02
sample63  -0.0596315364  4.137107e-02
sample64  -0.0449227251  2.600951e-03
sample65   0.0939382280  4.406949e-02
sample66   0.1063397797  5.710076e-02
sample67  -0.0201581000 -2.361746e-01
sample68   0.0037208285 -2.418539e-02
sample69  -0.0645161978  1.155618e-01
sample70  -0.1013439750  1.351780e-01
sample71  -0.0016466141  2.976775e-02
sample72   0.0328895361  2.835773e-02
sample73   0.0275080385  5.148153e-02
sample74   0.1341718397  7.895302e-02
sample75   0.0951576626  3.943149e-02
sample76  -0.0864719989 -3.035052e-02
sample77  -0.1035749507  2.545326e-02
sample78  -0.1575647796 -4.939478e-02
sample79   0.0189138345 -4.874690e-02
sample80   0.1384142728 -4.313994e-05
sample81  -0.0118846661  6.357909e-02
sample82  -0.1675306669 -3.533967e-02
sample83  -0.0065671196  7.812500e-02
sample84   0.1486890678  3.109095e-02
sample85  -0.0532720427 -7.417986e-02
sample86  -0.1138474964  1.822570e-05
sample87   0.0432865908 -6.080499e-02
sample88   0.0433451177 -1.402486e-01
sample89   0.0331204824  1.395428e-02
sample90  -0.0607413462  8.610386e-02
sample91  -0.0566263934 -1.303769e-01
sample92  -0.0359580740 -1.061605e-01
sample93  -0.0433646453  4.443610e-02
sample94  -0.0477292109  1.059571e-01
sample95  -0.0249595922  3.980510e-02
sample96   0.0035217610  9.293931e-02
sample97  -0.0066051933  1.527234e-01
sample98   0.0020367061  5.579516e-02
sample99  -0.0886621612  3.728370e-02
sample100 -0.1091259592  3.560402e-02
sample101 -0.0739723889  4.317888e-02
sample102  0.0574455820  2.784082e-02
sample103  0.0142733693 -9.706333e-03
sample104  0.0710395572 -4.068331e-02
sample105  0.0980829971  3.452996e-02
sample106 -0.0254260469 -3.628934e-02
sample107 -0.0160655004  9.173398e-02
sample108 -0.0200988297  2.379699e-02
sample109 -0.0389781918 -1.692313e-02
sample110 -0.0326305243 -2.988087e-02
sample111  0.0676935970  6.038248e-02
sample112  0.0167883511 -5.336924e-03
sample113  0.0969214019  2.757701e-02
sample114 -0.0026397983  9.209103e-02
sample115 -0.0308049522 -1.603746e-02
sample116 -0.1240306415 -1.272998e-01
sample117  0.0334728656 -5.392663e-02
sample118 -0.1037152176 -6.252439e-02
sample119 -0.1064170719 -1.196217e-01
sample120 -0.0771357652  1.004935e-01
sample121 -0.0129352281 -3.181916e-02
sample122  0.0847487660  5.568460e-02
sample123 -0.0041335544 -7.693542e-03
sample124 -0.0583462114  8.396474e-02
sample125  0.0634843282  5.232567e-02
sample126 -0.0662582070  1.091730e-01
sample127 -0.0865025592  1.094173e-01
sample128 -0.0627821931  1.471090e-02
sample129 -0.0336274627  4.007777e-02
sample130 -0.0293518105  8.046087e-02
sample131 -0.0469196811  2.209394e-03
sample132 -0.0241745526  1.248608e-01
sample133  0.0907303786 -1.466698e-02
sample134 -0.0350841250 -7.539660e-02
sample135  0.0001334851 -9.185807e-03
sample136 -0.0335874831  9.860184e-02
sample137 -0.0640147304  7.554374e-02
sample138  0.0060964064  1.742782e-02
sample139 -0.0592082799 -5.615005e-02
sample140  0.0427988548  1.099468e-02
sample141  0.0618793341  9.301100e-02
sample142  0.0898552550 -3.573326e-02
sample143  0.0817391022 -8.880528e-02
sample144  0.0787754482  3.821395e-02
sample145  0.1085819553 -1.569461e-01
sample146 -0.0589555065  4.373240e-02
sample147 -0.0495327965 -7.278036e-03
sample148  0.1161590537 -9.078161e-03
sample149 -0.0121575593 -7.788460e-02
sample150 -0.0314511989 -3.520220e-02
sample151  0.0575380971  1.945391e-02
sample152 -0.0494540398 -7.025565e-02
sample153 -0.0941338415 -2.153271e-01
sample154 -0.0335928899 -2.078822e-02
sample155  0.0690459016  2.780363e-02
sample156  0.1039902290  6.292489e-02
sample157 -0.0408645839 -8.065529e-03
sample158  0.1018106320 -7.817018e-03
sample159 -0.0281732485  1.207259e-02
sample160  0.1643052868 -2.977818e-03
sample161  0.0374330061 -8.524589e-02
sample162 -0.0804538201 -8.349638e-02
sample163 -0.0743232297  1.406343e-02
sample164  0.1208804318  2.139522e-02
sample165  0.1608115953 -2.025160e-02
sample166 -0.0425947860  2.660798e-02
sample167 -0.0226849505  4.464258e-02
sample168 -0.0180737327  7.471412e-04
sample169  0.0190780182 -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 
  11.70    0.31   12.00 

Example timings

STATegRa.Rcheck/examples_i386/STATegRa-Ex.timings

nameusersystemelapsed
STATegRaUsersGuide000
STATegRa_data0.410.010.70
STATegRa_data_TCGA_BRCA0.000.000.05
bioDist1.010.061.07
bioDistFeature0.600.040.63
bioDistFeaturePlot0.540.000.55
bioDistW0.490.010.53
bioDistWPlot0.510.000.51
bioMap000
combiningMappings0.020.000.02
createOmicsExpressionSet0.170.000.17
getInitialData0.640.160.80
getLoadings0.720.090.81
getMethodInfo0.660.080.73
getPreprocessing1.040.231.28
getScores0.600.130.72
getVAF0.560.140.71
holistOmics000
modelSelection1.810.342.15
omicsCompAnalysis4.110.144.25
omicsNPC000
plotRes5.230.115.35
plotVAF4.800.034.82

STATegRa.Rcheck/examples_x64/STATegRa-Ex.timings

nameusersystemelapsed
STATegRaUsersGuide000
STATegRa_data0.290.010.30
STATegRa_data_TCGA_BRCA0.000.020.02
bioDist0.780.000.78
bioDistFeature0.440.020.46
bioDistFeaturePlot0.530.010.54
bioDistW0.450.020.47
bioDistWPlot0.460.010.47
bioMap0.010.000.02
combiningMappings000
createOmicsExpressionSet0.120.020.14
getInitialData0.610.090.70
getLoadings0.550.130.68
getMethodInfo0.610.090.70
getPreprocessing0.810.221.03
getScores0.550.120.67
getVAF0.640.150.78
holistOmics000
modelSelection1.590.291.89
omicsCompAnalysis3.220.173.40
omicsNPC000
plotRes4.670.024.68
plotVAF3.800.053.85