##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:STATegRa.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings STATegRa_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/STATegRa.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘STATegRa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STATegRa’ version ‘1.24.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘STATegRa’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
modelSelection,list-numeric-character: no visible binding for global
  variable ‘components’
modelSelection,list-numeric-character: no visible binding for global
  variable ‘mylabel’
plotVAF,caClass: no visible binding for global variable ‘comp’
plotVAF,caClass: no visible binding for global variable ‘VAF’
plotVAF,caClass: no visible binding for global variable ‘block’
selectCommonComps,list-numeric: no visible binding for global variable
  ‘comps’
selectCommonComps,list-numeric: no visible binding for global variable
  ‘block’
selectCommonComps,list-numeric: no visible binding for global variable
  ‘comp’
selectCommonComps,list-numeric: no visible binding for global variable
  ‘ratio’
Undefined global functions or variables:
  VAF block comp components comps mylabel ratio
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘STATEgRa_Example.omicsCLUST.R’
  Running ‘STATEgRa_Example.omicsPCA.R’
  Running ‘STATegRa_Example.omicsNPC.R’
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/STATegRa.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL STATegRa
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘STATegRa’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (STATegRa)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 Oct 17 05:54:36 2020 
*********************************************** 
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 
  3.277   0.107   3.381 

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, 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 
 28.764   0.365  29.116 

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 82.609   0.165  82.759 

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ###########################################
> ########### EXAMPLE OF THE OMICSPCA
> ###########################################
> require(STATegRa)
Loading required package: STATegRa
> 
> # g_legend (not exported by STATegRa any more)
> ## code from https://github.com/hadley/ggplot2/wiki/Share-a-legend-between-two-ggplot2-graphs
> g_legend<-function(a.gplot){
+     tmp <- ggplot_gtable(ggplot_build(a.gplot))
+     leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
+     legend <- tmp$grobs[[leg]]
+     return(legend)}
> 
> #########################
> ## PART 1. Load data
> 
> ## Load data
> data(STATegRa_S3)
> 
> ls()
[1] "Block1.PCA" "Block2.PCA" "ed.PCA"     "g_legend"  
> 
> ## Create ExpressionSets
> # Block1 - Expression data
> B1 <- createOmicsExpressionSet(Data=Block1.PCA,pData=ed.PCA,pDataDescr=c("classname"))
> # Block2 - miRNA expression data
> B2 <- createOmicsExpressionSet(Data=Block2.PCA,pData=ed.PCA,pDataDescr=c("classname"))
> 
> #########################
> ## PART 2.  Model Selection
> 
> require(grid)
Loading required package: grid
> require(gridExtra)
Loading required package: gridExtra
> require(ggplot2)
Loading required package: ggplot2
> 
> ## Select the optimal components
> ms <- modelSelection(Input=list(B1,B2),Rmax=4,fac.sel="single%",varthreshold=0.03,center=TRUE,scale=TRUE,weight=TRUE)
Common components
[1] 2

Distinctive components
[[1]]
[1] 2

[[2]]
[1] 2

> 
> 
> #########################
> ## PART 3. Component Analysis
> 
> ## 3.1 Component analysis of the three methods
> discoRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),method="DISCOSCA",Rcommon=2,Rspecific=c(2,2),center=TRUE,
+                               scale=TRUE,weight=TRUE)
> jiveRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),method="JIVE",Rcommon=2,Rspecific=c(2,2),center=TRUE,
+                              scale=TRUE,weight=TRUE)
> o2plsRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),method="O2PLS",Rcommon=2,Rspecific=c(2,2),center=TRUE,
+                               scale=TRUE,weight=TRUE)
> 
> ## 3.2 Exploring scores structures
> 
> # Exploring DISCO-SCA scores structure
> discoRes@scores$common ## Common scores
                      1             2
sample1   -0.0781585719 -0.0431525672
sample2    0.1192219075  0.0294033181
sample3    0.0531404184 -0.0746858118
sample4   -0.0292973805 -0.0006010821
sample5   -0.0202089769  0.0110456206
sample6   -0.1226086357  0.1053469941
sample7   -0.1078929983 -0.0322441463
sample8   -0.1782890813  0.1449335187
sample9   -0.0468695449 -0.0455136178
sample10   0.0036031612  0.0420088108
sample11   0.0035567365 -0.0566257326
sample12  -0.1006134855  0.0641413452
sample13   0.1174419355  0.0907486879
sample14  -0.0981202182  0.0617741308
sample15  -0.0085338255 -0.0086951289
sample16  -0.0783143623  0.1581332339
sample17   0.1483610483  0.0638573232
sample18   0.0963086150  0.0556649329
sample19   0.0217238118 -0.0720134068
sample20   0.0635635676 -0.0779603129
sample21   0.0201846561  0.1566374875
sample22  -0.0218275975 -0.0764089018
sample23  -0.0852043508 -0.0032730210
sample24   0.1287182583  0.1924503876
sample25   0.0430571938 -0.0456632538
sample26   0.1453896133  0.0541494852
sample27   0.0197484863 -0.1185620883
sample28   0.1025339682  0.0650680089
sample29  -0.0706025134 -0.0682913126
sample30   0.1295627787 -0.0066742103
sample31  -0.1147447868  0.1232697406
sample32   0.0374311225  0.0380212827
sample33  -0.0599521253  0.0136875949
sample34   0.0984200286  0.0375350058
sample35   0.0543103890 -0.0378055703
sample36  -0.1403614204 -0.0343690425
sample37  -0.0228933066 -0.0732774706
sample38   0.0222068805 -0.0962565087
sample39   0.0941736971  0.0215192407
sample40  -0.0643794105 -0.0687802056
sample41   0.0327632254 -0.1232190670
sample42   0.0500427891 -0.0292524349
sample43   0.0184497791  0.0233018038
sample44  -0.1487891211  0.1171265377
sample45   0.1050777233  0.1123161484
sample46   0.1151190865 -0.1094014372
sample47   0.0962593277 -0.0288423933
sample48  -0.0004836401 -0.0310314602
sample49  -0.1135201521  0.1213917192
sample50   0.0123542376 -0.1740717931
sample51  -0.0550520751  0.1258933555
sample52  -0.0499110398  0.0728595530
sample53  -0.1119769320  0.1588048590
sample54   0.0360057538  0.0228567787
sample55  -0.0210416496  0.0006756367
sample56   0.0434175283  0.0633137984
sample57  -0.0197811109  0.1150775933
sample58  -0.0030438868  0.0326105945
sample59  -0.0500249986  0.0129470518
sample60  -0.0184267218  0.0136221557
sample61  -0.0150291189  0.0635098969
sample62   0.0304759888 -0.0201284226
sample63  -0.1102253036  0.1285999098
sample64  -0.1552587313  0.0971206217
sample65   0.0058501803  0.0207120336
sample66   0.0025607344  0.0424277777
sample67  -0.1546624637 -0.0661622945
sample68  -0.0536370376 -0.0923646709
sample69  -0.0640336793  0.0081984606
sample70  -0.0163528869 -0.0663240116
sample71   0.0102531486 -0.1345957249
sample72   0.0654195585 -0.0196087681
sample73   0.1048553745  0.0220980503
sample74  -0.0123799333  0.0586138368
sample75  -0.0392080032 -0.0209729890
sample76  -0.0648951629 -0.0524799845
sample77  -0.1172921217 -0.0201248279
sample78   0.1463071881  0.0708415574
sample79  -0.0265214134 -0.1603378508
sample80  -0.0279739024 -0.0214134688
sample81  -0.0079216854 -0.0738493327
sample82   0.1544235701 -0.0361477770
sample83   0.0494208416 -0.0050006114
sample84   0.0259038246 -0.0346579578
sample85  -0.1116478996 -0.0031462970
sample86   0.1306480973 -0.0377198934
sample87   0.0554781926 -0.0459758925
sample88   0.0301635061  0.0382192822
sample89   0.1016869446  0.0694054367
sample90  -0.0086823650 -0.0201357059
sample91  -0.1578634783 -0.2097712310
sample92  -0.0170938097 -0.1655878862
sample93   0.0979802335 -0.0121499993
sample94  -0.0131491550 -0.0114929928
sample95  -0.0315687853 -0.0758898081
sample96  -0.0024131632 -0.0470178186
sample97  -0.0634552198  0.0270303500
sample98   0.0359370249 -0.0135468933
sample99   0.1009164939  0.1124726761
sample100 -0.0551755332  0.0246489532
sample101  0.0080106858 -0.1627369631
sample102  0.0046445095  0.0095525536
sample103  0.0472519562 -0.0940379909
sample104 -0.0198158555 -0.0591119954
sample105  0.0400239448 -0.0160964790
sample106  0.0923811612  0.0369006114
sample107  0.1019369370  0.0224957449
sample108  0.0877089378 -0.0128845168
sample109 -0.0864829045 -0.0901005204
sample110  0.1223116544 -0.0096104687
sample111 -0.0257361011 -0.0936230444
sample112  0.0765288236  0.0270364613
sample113 -0.0258802370  0.0377470456
sample114 -0.0021146421 -0.0882044980
sample115 -0.0303463788 -0.0723660068
sample116 -0.0780505697 -0.0685122466
sample117 -0.0536895790 -0.0912000886
sample118 -0.0666650303 -0.0236246033
sample119 -0.1021881169 -0.2324909382
sample120 -0.0750221399  0.0243345493
sample121  0.0756938483  0.0942997019
sample122  0.0259629997  0.0731937605
sample123  0.1037846509 -0.0369203916
sample124 -0.0611211463  0.0421671753
sample125  0.0738473661  0.0066914581
sample126 -0.0972922454  0.0762694422
sample127 -0.0824705067 -0.0096648517
sample128  0.1249407474  0.0929295657
sample129  0.0734064966 -0.0434358913
sample130  0.0003497957 -0.0309882078
sample131 -0.0930183303  0.0155960955
sample132 -0.0736226390  0.0732983240
sample133  0.0498398954 -0.0462453859
sample134 -0.1644868506  0.0720052614
sample135  0.0752296607  0.0003859605
sample136 -0.0227153258 -0.0495492300
sample137 -0.0564722177 -0.0288902680
sample138 -0.0255990344 -0.0610911910
sample139 -0.0621211739  0.0235805921
sample140  0.0604148958 -0.0435536097
sample141 -0.0246744334  0.0532616563
sample142  0.0409565445  0.0316248696
sample143  0.0077359836 -0.0476902775
sample144 -0.0173242481 -0.0156780196
sample145 -0.0485461128  0.1202778419
sample146 -0.0419651787 -0.0811262549
sample147  0.0977309388 -0.0274830716
sample148 -0.0368249725  0.0803965241
sample149  0.0072865138 -0.1533015704
sample150 -0.1020821310  0.0624805185
sample151 -0.0305399822 -0.0289318096
sample152  0.0533592209 -0.0638287589
sample153  0.0891640341  0.1799561375
sample154  0.0727554871 -0.0834144180
sample155  0.0880667187 -0.0220791717
sample156  0.0276556010 -0.0326590489
sample157  0.1155031555  0.0183637330
sample158  0.0281508183 -0.0104910639
sample159 -0.0663232856  0.0443796267
sample160  0.0302647693  0.0404294565
sample161 -0.0114711887 -0.0591063599
sample162  0.1337092810  0.1398166376
sample163 -0.1330121175  0.1688790905
sample164  0.0150337792  0.0028382950
sample165 -0.0076517224 -0.0164135693
sample166 -0.0367792937  0.0630620232
sample167 -0.1111991571  0.0030063969
sample168  0.0672984661  0.0446250915
sample169  0.0413007148  0.0224430893
> discoRes@scores$dist[[1]] ## Distinctive scores for Block 1
                      1             2
sample1    0.0420498498  0.0867867581
sample2    0.0820830498 -0.0410998637
sample3   -0.0155947836 -0.0195157411
sample4    0.1001329098 -0.0410808977
sample5    0.0153467220 -0.0253266758
sample6   -0.0340292368 -0.0408240441
sample7   -0.0722595365  0.0002353074
sample8    0.0457552608 -0.0370060735
sample9    0.0086258628  0.0820187805
sample10   0.0423613891 -0.0083941294
sample11  -0.0022547621  0.0787775848
sample12  -0.0322056247  0.1479818897
sample13   0.0293937399 -0.0306777327
sample14  -0.0337467308 -0.0367513998
sample15  -0.0815517697  0.1275642297
sample16  -0.0508370564  0.0540578507
sample17  -0.0062570906  0.0041015272
sample18  -0.0705628468 -0.0351040818
sample19   0.0476790414 -0.0509588844
sample20  -0.0522974538  0.0715549172
sample21   0.0119186665 -0.0376129864
sample22  -0.0724437919 -0.0095589825
sample23   0.0992531372  0.0134267165
sample24   0.1595231420  0.0728583541
sample25   0.0920653220 -0.0749764453
sample26   0.0595580642  0.0848945119
sample27  -0.0826539242 -0.0086691179
sample28   0.0384830224  0.0440945098
sample29  -0.0777665462  0.1735339188
sample30  -0.1229494159 -0.0818974113
sample31  -0.0579804902 -0.0238659454
sample32  -0.0970381594 -0.0111412365
sample33  -0.1017609579 -0.0630420083
sample34  -0.0637900543  0.0377949864
sample35  -0.0789993189 -0.0229701186
sample36  -0.1224962438 -0.1274930894
sample37  -0.1798873047 -0.1673378644
sample38  -0.0466333694  0.0888194963
sample39   0.0168703356  0.0421528333
sample40  -0.1756442496 -0.1526595224
sample41  -0.0042427211  0.0004958602
sample42   0.0447814657 -0.0651504053
sample43  -0.0482308636 -0.0253522155
sample44   0.1986758973 -0.0545850912
sample45   0.0741885162  0.0054665346
sample46  -0.0478821829 -0.0007034393
sample47  -0.0608187589  0.0481643001
sample48   0.1381494716  0.0578262721
sample49   0.0530541387 -0.1405572676
sample50   0.0173755755  0.1602425490
sample51  -0.0462489507  0.0303450884
sample52  -0.0280010141  0.0280370874
sample53  -0.0667548847  0.0237679393
sample54  -0.0121834937 -0.0521356046
sample55  -0.0182385362  0.0221329528
sample56   0.0001291361  0.0030891445
sample57  -0.0316593423  0.0530163669
sample58  -0.0393911871 -0.0297797055
sample59  -0.1278294129 -0.0546505568
sample60  -0.1486930350  0.1069175760
sample61  -0.0793068780  0.0569793984
sample62  -0.1172820104 -0.0149165679
sample63   0.0028805904  0.1300490151
sample64  -0.0237300311  0.1073268357
sample65   0.0126554934  0.0589801691
sample66   0.0468194416 -0.0771091363
sample67  -0.1494288514 -0.0769824512
sample68  -0.0978012048 -0.0577311486
sample69  -0.0403093047  0.0156052089
sample70  -0.0221569360  0.0315465774
sample71   0.0546366377 -0.0272376783
sample72  -0.1107509743 -0.0537289354
sample73  -0.0906743174  0.0579984676
sample74  -0.0586530911  0.0121422032
sample75  -0.0390496389  0.0349295313
sample76   0.0022902264 -0.1676549006
sample77   0.0232037937 -0.2067303775
sample78   0.0929777707 -0.0434972059
sample79   0.1619422923 -0.0378115364
sample80  -0.0680340969  0.1424680742
sample81   0.0530737403 -0.0358343588
sample82  -0.0266851144 -0.0577427442
sample83  -0.1517254544 -0.0448517087
sample84   0.0570946869 -0.0273817694
sample85  -0.1086311770 -0.1228099687
sample86  -0.0833888929 -0.0442884754
sample87  -0.0022051955 -0.0943897423
sample88   0.0078231898 -0.1140521258
sample89  -0.0611028974 -0.0094585360
sample90  -0.0022966773 -0.0936245659
sample91  -0.0433603918  0.3206031878
sample92   0.1815264311 -0.0334685555
sample93  -0.0267628257  0.0614441479
sample94  -0.0181881230  0.0605100633
sample95   0.0720337443 -0.0013043141
sample96   0.0559682724 -0.0118789843
sample97   0.0217412414  0.0195407283
sample98  -0.0379176022  0.0588370835
sample99   0.0792468010 -0.0151311552
sample100 -0.0222112289 -0.0023321010
sample101  0.0387176832  0.1224256745
sample102  0.2094606204 -0.0516489081
sample103 -0.0138515009  0.0301076464
sample104  0.0807963112 -0.0162725493
sample105  0.0520459253 -0.1229671735
sample106  0.0192628508 -0.0185249538
sample107 -0.0319007602  0.0405130461
sample108  0.0140686086  0.0163424122
sample109  0.1831903923  0.0612986609
sample110  0.0292784171 -0.0199851248
sample111  0.1423213658  0.0327331615
sample112 -0.0426320518 -0.0029079122
sample113  0.0771926835  0.0268708054
sample114  0.0241589696 -0.0184062793
sample115  0.1958994149  0.0460104177
sample116  0.1394443177 -0.0530824838
sample117  0.1672297807 -0.1386555016
sample118  0.0448334516 -0.0117628610
sample119  0.0910339527  0.2217460921
sample120  0.0331390139 -0.0057284421
sample121 -0.0307500683  0.1392492702
sample122  0.0839804211 -0.0292027225
sample123 -0.0239679746 -0.0642148370
sample124  0.0909162513  0.0130392790
sample125  0.0065327200 -0.1092632079
sample126 -0.0935261054  0.1368289263
sample127 -0.0035398617  0.0292761389
sample128  0.0660355411  0.1018535246
sample129 -0.0693677275 -0.0695393962
sample130 -0.0008529856 -0.0669694209
sample131 -0.0431014905  0.0174069195
sample132  0.0637060601  0.0029347597
sample133  0.0289469771 -0.0390815080
sample134 -0.0446155324  0.0456322315
sample135 -0.0712324715  0.0521651363
sample136 -0.0596298938  0.0197326308
sample137 -0.0793181760 -0.0380602893
sample138  0.0973510110 -0.0454225415
sample139 -0.0539923356 -0.1534323660
sample140 -0.0850825709  0.0955843627
sample141  0.0192686263 -0.0554464173
sample142  0.0672271892 -0.0461343632
sample143  0.0303708817 -0.0519259735
sample144  0.0089359174  0.0145816578
sample145  0.0638843411  0.0122210444
sample146 -0.0585896542  0.0063115207
sample147 -0.0894170039 -0.1124588108
sample148  0.0216393172 -0.0615992051
sample149  0.0515342083 -0.0839882532
sample150 -0.0568255946 -0.0124473755
sample151  0.0789513634 -0.0261842188
sample152  0.0330758634  0.1306450109
sample153  0.1752060914  0.1497650156
sample154 -0.0421460831 -0.0036981338
sample155 -0.0680185986  0.0095732742
sample156 -0.0388906225  0.1057580139
sample157 -0.0314749490  0.0561372649
sample158 -0.0329614202  0.0353955952
sample159  0.0398412717 -0.1007392902
sample160 -0.0424913981  0.0108494990
sample161  0.0888339728 -0.0679709412
sample162  0.0027570135  0.1237812911
sample163  0.0126192034  0.0725392341
sample164  0.0566772244 -0.0458337182
sample165  0.0315330183 -0.0236367972
sample166  0.0612073258 -0.0425259642
sample167 -0.0142729631  0.0179310034
sample168  0.0169506282 -0.0769629855
sample169 -0.0675064575  0.0131514512
> discoRes@scores$dist[[2]] ## Distinctive scores for Block 2
                      1             2
sample1   -0.0012328614 -1.635707e-01
sample2   -0.0724355943 -6.023149e-03
sample3   -0.0188458497 -1.080025e-01
sample4    0.0390142655  3.104159e-04
sample5    0.1774810279 -2.996439e-02
sample6   -0.0451448195 -3.455949e-02
sample7   -0.0226461250 -7.018386e-03
sample8   -0.1033687028 -9.858760e-03
sample9    0.1350016586  8.979198e-02
sample10   0.1259883142 -5.097984e-02
sample11   0.0979793095  7.086642e-02
sample12  -0.0863019730 -8.620284e-02
sample13  -0.1381406210  1.827984e-01
sample14  -0.0615075561 -2.642830e-02
sample15   0.0381602631 -3.101529e-02
sample16  -0.0048781949  1.270269e-03
sample17  -0.0788486346 -1.547713e-02
sample18  -0.0884192019 -3.795558e-02
sample19   0.0703044661 -1.084000e-01
sample20  -0.0025579170  7.976048e-02
sample21   0.0941591960 -4.127046e-02
sample22  -0.0550268340 -7.806533e-02
sample23   0.0679493671 -4.102059e-02
sample24  -0.1310975893  1.649260e-01
sample25   0.0113583260 -4.426923e-02
sample26  -0.1402951165  2.016373e-02
sample27   0.0261569131  1.591045e-03
sample28  -0.0724203321  5.850423e-02
sample29  -0.0330050097  2.063664e-03
sample30  -0.0228751931 -2.015388e-02
sample31  -0.0635072366 -6.670427e-02
sample32   0.0685098930 -4.955273e-02
sample33  -0.0777764749 -1.272069e-01
sample34   0.0157840768 -3.024352e-02
sample35  -0.0529627768  1.500983e-01
sample36   0.0070909000  2.025327e-01
sample37  -0.0442411180  1.802114e-01
sample38  -0.0781504894 -3.676187e-02
sample39   0.0120328987 -3.388926e-02
sample40  -0.0473282693  1.471588e-01
sample41   0.0228195143 -2.673365e-02
sample42  -0.0245362329 -7.960904e-02
sample43   0.1036361261 -8.229600e-02
sample44  -0.1012237711  7.049133e-02
sample45   0.0013722509 -2.451217e-02
sample46  -0.0558504637  2.949173e-03
sample47  -0.0380478316  4.554254e-02
sample48   0.0784341334  4.888909e-02
sample49  -0.0605171752 -1.162592e-02
sample50   0.0530089071 -2.737620e-02
sample51   0.1514643017  5.678197e-02
sample52   0.1860934791  1.246709e-01
sample53  -0.0064182150 -2.701130e-02
sample54   0.0697036110 -2.308459e-02
sample55   0.1633578185  1.366454e-02
sample56   0.1011481833  4.682067e-02
sample57   0.1730371982  1.609588e-01
sample58  -0.0071385865 -1.666979e-02
sample59  -0.0030458497  3.005393e-02
sample60   0.0215843199  2.665894e-01
sample61   0.1510584534  1.002383e-01
sample62  -0.0925531038 -4.845704e-02
sample63  -0.0596316172 -4.137134e-02
sample64  -0.0449226951 -2.600802e-03
sample65   0.0939382326 -4.406951e-02
sample66   0.1063395709 -5.710149e-02
sample67  -0.0201578236  2.361758e-01
sample68   0.0037211031  2.418642e-02
sample69  -0.0645161014 -1.155615e-01
sample70  -0.1013437166 -1.351773e-01
sample71  -0.0016463120 -2.976685e-02
sample72   0.0328895094 -2.835772e-02
sample73   0.0275079761 -5.148170e-02
sample74   0.1341717450 -7.895328e-02
sample75   0.0951578191 -3.943094e-02
sample76  -0.0864719784  3.035063e-02
sample77  -0.1035750032 -2.545342e-02
sample78  -0.1575652137  4.939323e-02
sample79   0.0189141779  4.874787e-02
sample80   0.1384145406  4.408981e-05
sample81  -0.0118845103 -6.357867e-02
sample82  -0.1675307904  3.533925e-02
sample83  -0.0065671349 -7.812494e-02
sample84   0.1486890859 -3.109095e-02
sample85  -0.0532720195  7.418013e-02
sample86  -0.1138475482 -1.835704e-05
sample87   0.0432865441  6.080487e-02
sample88   0.0433448350  1.402478e-01
sample89   0.0331202064 -1.395513e-02
sample90  -0.0607413704 -8.610398e-02
sample91  -0.0566253239  1.303805e-01
sample92  -0.0359577386  1.061614e-01
sample93  -0.0433646315 -4.443610e-02
sample94  -0.0477290769 -1.059567e-01
sample95  -0.0249593799 -3.980450e-02
sample96   0.0035218689 -9.293907e-02
sample97  -0.0066051620 -1.527233e-01
sample98   0.0020367921 -5.579489e-02
sample99  -0.0886626088 -3.728530e-02
sample100 -0.1091259552 -3.560400e-02
sample101 -0.0739718386 -4.317719e-02
sample102  0.0574454179 -2.784157e-02
sample103  0.0142736072  9.707105e-03
sample104  0.0710396800  4.068366e-02
sample105  0.0980828497 -3.453049e-02
sample106 -0.0254262758  3.628857e-02
sample107 -0.0160655964 -9.173434e-02
sample108 -0.0200988714 -2.379718e-02
sample109 -0.0389778686  1.692400e-02
sample110 -0.0326306649  2.988036e-02
sample111  0.0676938631 -6.038179e-02
sample112  0.0167882113  5.336500e-03
sample113  0.0969213316 -2.757731e-02
sample114 -0.0026395756 -9.209038e-02
sample115 -0.0308047567  1.603789e-02
sample116 -0.1240305093  1.273001e-01
sample117  0.0334729407  5.392676e-02
sample118 -0.1037151248  6.252468e-02
sample119 -0.1064161584  1.196246e-01
sample120 -0.0771357547 -1.004935e-01
sample121 -0.0129354010  3.181861e-02
sample122  0.0847484877 -5.568561e-02
sample123 -0.0041336263  7.693315e-03
sample124 -0.0583462679 -8.396505e-02
sample125  0.0634841200 -5.232637e-02
sample126 -0.0662581059 -1.091726e-01
sample127 -0.0865023964 -1.094168e-01
sample128 -0.0627824852 -1.471199e-02
sample129 -0.0336274658 -4.007774e-02
sample130 -0.0293517877 -8.046084e-02
sample131 -0.0469195890 -2.209031e-03
sample132 -0.0241746729 -1.248613e-01
sample133  0.0907303936  1.466701e-02
sample134 -0.0350840895  7.539684e-02
sample135  0.0001334882  9.185867e-03
sample136 -0.0335872666 -9.860113e-02
sample137 -0.0640145922 -7.554323e-02
sample138  0.0060965115 -1.742758e-02
sample139 -0.0592084318  5.614968e-02
sample140  0.0427990464 -1.099400e-02
sample141  0.0618791650 -9.301159e-02
sample142  0.0898550456  3.573254e-02
sample143  0.0817391390  8.880542e-02
sample144  0.0787755266 -3.821371e-02
sample145  0.1085816487  1.569452e-01
sample146 -0.0589552093 -4.373140e-02
sample147 -0.0495329139  7.277733e-03
sample148  0.1161588010  9.077364e-03
sample149 -0.0121572816  7.788549e-02
sample150 -0.0314512553  3.520212e-02
sample151  0.0575381501 -1.945382e-02
sample152 -0.0494538079  7.025636e-02
sample153 -0.0941343555  2.153252e-01
sample154 -0.0335927345  2.078875e-02
sample155  0.0690459095 -2.780356e-02
sample156  0.1039904271 -6.292425e-02
sample157 -0.0408646822  8.065199e-03
sample158  0.1018106805  7.817216e-03
sample159 -0.0281734203 -1.207316e-02
sample160  0.1643051751  2.977520e-03
sample161  0.0374330538  8.524601e-02
sample162 -0.0804542135  8.349508e-02
sample163 -0.0743234647 -1.406419e-02
sample164  0.1208803399 -2.139557e-02
sample165  0.1608116059  2.025164e-02
sample166 -0.0425949816 -2.660868e-02
sample167 -0.0226848097 -4.464211e-02
sample168 -0.0180740125 -7.480775e-04
sample169  0.0190779515  2.645412e-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 
 13.389   0.127  13.502