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CHECK report for MLP on tokay1

This page was generated on 2019-04-13 11:21:26 -0400 (Sat, 13 Apr 2019).

Package 983/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MLP 1.30.0
Tobias Verbeke
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/MLP
Branch: RELEASE_3_8
Last Commit: f48b881
Last Changed Date: 2018-10-30 11:41:46 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
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: MLP
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLP.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MLP_1.30.0.tar.gz
StartedAt: 2019-04-13 03:55:43 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:02:40 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 417.7 seconds
RetCode: 0
Status:  OK  
CheckDir: MLP.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLP.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MLP_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MLP.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 'MLP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MLP' version '1.30.0'
* 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'
 NOTE
Depends: includes the non-default packages:
  'AnnotationDbi' 'affy' 'plotrix' 'gplots' 'gmodels' 'gdata' 'gtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'MLP' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'gdata' 'gmodels' 'gplots' 'gtools'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'GO.db' 'GOstats' 'KEGG.db' 'Rgraphviz' 'annotate' 'org.Cf.eg.db'
  'org.Hs.eg.db' 'org.Mm.eg.db' 'org.Rn.eg.db' 'reactome.db'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'affy' 'gdata' 'gmodels' 'gplots' 'gtools' 'plotrix'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MLP: no visible global function definition for 'na.omit'
addGeneSetDescription: no visible binding for global variable 'GOTERM'
addGeneSetDescription: no visible binding for global variable
  'KEGGPATHID2NAME'
addGeneSetDescription: no visible binding for global variable
  'reactomePATHNAME2ID'
getGeneSets: no visible binding for global variable
  'org.Mm.egGO2ALLEGS'
getGeneSets: no visible binding for global variable
  'org.Hs.egGO2ALLEGS'
getGeneSets: no visible binding for global variable
  'org.Rn.egGO2ALLEGS'
getGeneSets: no visible binding for global variable
  'org.Cf.egGO2ALLEGS'
getGeneSets: no visible binding for global variable 'GOBPANCESTOR'
getGeneSets: no visible binding for global variable 'GOMFANCESTOR'
getGeneSets: no visible binding for global variable 'GOCCANCESTOR'
getGeneSets: no visible binding for global variable 'GOTERM'
getGeneSets: no visible binding for global variable 'KEGGPATHID2EXTID'
getGeneSets: no visible binding for global variable 'KEGGPATHID2NAME'
getGeneSets: no visible binding for global variable
  'reactomePATHNAME2ID'
getGeneSets: no visible binding for global variable
  'reactomePATHID2EXTID'
mlpBarplot: no visible global function definition for 'par'
mlpBarplot: no visible global function definition for 'barplot'
mlpBarplot: no visible global function definition for 'title'
plotGOgraph: no visible global function definition for 'GOGraph'
plotGOgraph: no visible global function definition for 'removeNode'
plotGOgraph: no visible global function definition for 'nodes'
plotGOgraph: no visible global function definition for 'layoutGraph'
plotGOgraph: no visible global function definition for 'colorpanel'
plotGOgraph: no visible global function definition for
  'nodeRenderInfo<-'
plotGOgraph: no visible global function definition for 'getGOTerm'
plotGOgraph: no visible global function definition for 'edgeRenderInfo'
plotGOgraph: no visible global function definition for
  'edgeRenderInfo<-'
plotGOgraph: no visible global function definition for
  'graphRenderInfo'
plotGOgraph: no visible global function definition for
  'graphRenderInfo<-'
plotGOgraph: no visible global function definition for 'edges'
plotGOgraph: no visible global function definition for 'renderGraph'
plotGOgraph: no visible global function definition for 'legend'
plotGeneSetSignificance: no visible global function definition for
  'lookUp'
plotGeneSetSignificance: no visible global function definition for
  'barplot'
plotQuantileCurves: no visible global function definition for 'plot'
plotQuantileCurves: no visible global function definition for 'axis'
plotQuantileCurves: no visible global function definition for 'par'
plotQuantileCurves: no visible global function definition for 'points'
plotQuantileCurves: no visible global function definition for 'text'
plotQuantileCurves: no visible global function definition for
  'matlines'
quantileCurves: no visible binding for global variable 'quantile'
quantileCurves: no visible global function definition for 'predict'
quantileCurves: no visible global function definition for
  'smooth.spline'
quantileCurves : tt: no visible global function definition for
  'smooth.spline'
quantileCurves : tt: no visible global function definition for
  'predict'
quantileCurves : tt: no visible global function definition for
  'quantile'
quantileCurves : vv: no visible global function definition for
  'smooth.spline'
quantileCurves : vv: no visible global function definition for
  'quantile'
quantileCurves : vv: no visible global function definition for
  'predict'
smdecreasing1: no visible global function definition for 'approx'
smdecreasing1: no visible global function definition for 'lsfit'
Undefined global functions or variables:
  GOBPANCESTOR GOCCANCESTOR GOGraph GOMFANCESTOR GOTERM
  KEGGPATHID2EXTID KEGGPATHID2NAME approx axis barplot colorpanel
  edgeRenderInfo edgeRenderInfo<- edges getGOTerm graphRenderInfo
  graphRenderInfo<- layoutGraph legend lookUp lsfit matlines na.omit
  nodeRenderInfo<- nodes org.Cf.egGO2ALLEGS org.Hs.egGO2ALLEGS
  org.Mm.egGO2ALLEGS org.Rn.egGO2ALLEGS par plot points predict
  quantile reactomePATHID2EXTID reactomePATHNAME2ID removeNode
  renderGraph smooth.spline text title
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "matlines", "par",
             "plot", "points", "text", "title")
  importFrom("stats", "approx", "lsfit", "na.omit", "predict",
             "quantile", "smooth.spline")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
getGeneSets 18.31   3.67  105.55
MLP         18.78   0.80   19.80
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
getGeneSets 19.84   0.97   20.81
MLP         19.59   0.70   20.30
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.MLP.R'
 OK
** running tests for arch 'x64' ...
  Running 'test.MLP.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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/MLP.Rcheck/00check.log'
for details.



Installation output

MLP.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MLP_1.30.0.tar.gz && rm -rf MLP.buildbin-libdir && mkdir MLP.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MLP.buildbin-libdir MLP_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MLP_1.30.0.zip && rm MLP_1.30.0.tar.gz MLP_1.30.0.zip
###
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  % 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 4303k  100 4303k    0     0  54.0M      0 --:--:-- --:--:-- --:--:-- 56.7M

install for i386

* installing *source* package 'MLP' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MLP'
    finding HTML links ... done
    MLP                                     html  
    addGeneSetDescription                   html  
    getGeneSets                             html  
    mlpBarplot                              html  
    plot.MLP                                html  
    plotGOgraph                             html  
    plotGeneSetSignificance                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MLP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MLP' as MLP_1.30.0.zip
* DONE (MLP)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MLP' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

MLP.Rcheck/tests_i386/test.MLP.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.

> require(MLP)	
Loading required package: MLP
Loading required package: AnnotationDbi
Loading required package: stats4
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

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: affy
Loading required package: plotrix
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:plotrix':

    plotCI

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess

Loading required package: gmodels
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

The following object is masked from 'package:IRanges':

    trim

The following objects are masked from 'package:S4Vectors':

    first, first<-

The following object is masked from 'package:Biobase':

    combine

The following object is masked from 'package:BiocGenerics':

    combine

The following object is masked from 'package:stats4':

    nobs

The following object is masked from 'package:stats':

    nobs

The following object is masked from 'package:utils':

    object.size

The following object is masked from 'package:base':

    startsWith

Loading required package: gtools
> set.seed(479)
> 
> # This is just the expressionset for this experiment.
> 
> pathExampleData <- system.file("exampleFiles", "expressionSetGcrma.rda", package = "MLP")
> load(pathExampleData)
> 
> # Libraries needed
> library(limma)

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

> library(org.Mm.eg.db) # for mouse

> 
> exprs(expressionSetGcrma)[1:2,]
              2760     2763     2765     2766     2768     2769     2761
100009600 2.371111 2.170060 2.233383 2.180717 2.325886 2.239441 2.297301
100012    2.176163 2.318876 2.419263 2.223307 2.585125 2.346060 2.292061
              2762    2764     2767     2770     2771
100009600 2.409001 2.49458 2.115814 2.371262 2.267459
100012    2.336415 2.47979 2.361981 2.330418 2.520918
> #              2760     2763     2765     2766     2768     2769     2761     2762    2764     2767
> #100009600 2.371111 2.170060 2.233383 2.180717 2.325886 2.239441 2.297301 2.409001 2.49458 2.115814
> #100012    2.176163 2.318876 2.419263 2.223307 2.585125 2.346060 2.292061 2.336415 2.47979 2.361981
> #              2770     2771
> #100009600 2.371262 2.267459
> #100012    2.330418 2.520918
> 
> pData(expressionSetGcrma)
     sample subGroup sampleColor subGroup1
2760      1        1     #FF0000        WT
2763      4        1     #FF0000        WT
2765      6        1     #FF0000        WT
2766      7        1     #FF0000        WT
2768      9        1     #FF0000        WT
2769     10        1     #FF0000        WT
2761      2        2     #0000FF        KO
2762      3        2     #0000FF        KO
2764      5        2     #0000FF        KO
2767      8        2     #0000FF        KO
2770     11        2     #0000FF        KO
2771     12        2     #0000FF        KO
> #     sample subGroup sampleColor
> #2760      1        1     #FF0000
> #2763      4        1     #FF0000
> #2765      6        1     #FF0000
> #2766      7        1     #FF0000
> #2768      9        1     #FF0000
> #2769     10        1     #FF0000
> #2761      2        2     #0000FF
> #2762      3        2     #0000FF
> #2764      5        2     #0000FF
> #2767      8        2     #0000FF
> #2770     11        2     #0000FF
> #2771     12        2     #0000FF
> 
> pData(expressionSetGcrma)$subGroup1 <- ifelse(pData(expressionSetGcrma)$subGroup==1,"WT","KO")
> 
> ###==============================================GENERATING LIMMA p-VALUES=================================
> 
> # boxplot(data.frame(exprs(expressionSetGcrma))
> normDat  <- normalizeQuantiles(exprs(expressionSetGcrma), ties=TRUE)
> subGroup <- pData(expressionSetGcrma)$subGroup
> design <- model.matrix(˜ -1 +factor(subGroup ))
> 
> colnames(design) <- c("group1", "group2")
> contrast.matrix <- makeContrasts(group1-group2, levels=design)
> fit <- lmFit(normDat,design)
> fit2 <- contrasts.fit(fit, contrast.matrix)
> fit2 <- eBayes(fit2)
> normDat.p <- fit2$p.value
> 
> normDat.p[1:5]
[1] 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761
> #[1] 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761
> 
> system.time(goGeneSet <- getGeneSets(species = "Mouse", geneSetSource = "GOBP", entrezIdentifiers = featureNames(expressionSetGcrma)))
Loading required package: GO.db

   user  system elapsed 
  21.66    3.23   24.89 
> goGeneSet[1:3]
$`GO:0000002`
 [1] "11545"  "16882"  "17258"  "17527"  "18975"  "19017"  "19819"  "22059" 
 [9] "23797"  "27393"  "27395"  "27397"  "50776"  "57813"  "66592"  "70556" 
[17] "72170"  "72962"  "74143"  "74244"  "74528"  "83408"  "83945"  "192287"
[25] "216021" "216805" "226153" "229524" "230784" "327762" "381760" "382985"
[33] "408022"

$`GO:0000003`
   [1] "11287"     "11352"     "11421"     "11430"     "11434"     "11441"    
   [7] "11477"     "11479"     "11480"     "11486"     "11495"     "11497"    
  [13] "11504"     "11516"     "11517"     "11535"     "11551"     "11552"    
  [19] "11553"     "11576"     "11600"     "11606"     "11614"     "11622"    
  [25] "11625"     "11647"     "11651"     "11674"     "11705"     "11757"    
  [31] "11789"     "11797"     "11804"     "11819"     "11820"     "11835"    
  [37] "11839"     "11857"     "11863"     "11865"     "11883"     "11920"    
  [43] "11998"     "12009"     "12018"     "12028"     "12034"     "12043"    
  [49] "12048"     "12050"     "12053"     "12124"     "12125"     "12142"    
  [55] "12144"     "12155"     "12159"     "12160"     "12161"     "12162"    
  [61] "12163"     "12164"     "12166"     "12167"     "12168"     "12173"    
  [67] "12190"     "12192"     "12211"     "12235"     "12236"     "12237"    
  [73] "12261"     "12305"     "12310"     "12316"     "12317"     "12323"    
  [79] "12344"     "12363"     "12366"     "12380"     "12387"     "12394"    
  [85] "12411"     "12416"     "12426"     "12427"     "12443"     "12447"    
  [91] "12448"     "12449"     "12458"     "12461"     "12462"     "12464"    
  [97] "12465"     "12466"     "12468"     "12469"     "12505"     "12527"    
 [103] "12530"     "12531"     "12532"     "12550"     "12566"     "12576"    
 [109] "12577"     "12589"     "12591"     "12592"     "12593"     "12606"    
 [115] "12608"     "12617"     "12638"     "12640"     "12659"     "12702"    
 [121] "12704"     "12705"     "12745"     "12753"     "12767"     "12801"    
 [127] "12804"     "12841"     "12846"     "12877"     "12916"     "12918"    
 [133] "12919"     "12946"     "12977"     "12981"     "13006"     "13030"    
 [139] "13039"     "13046"     "13052"     "13070"     "13075"     "13123"    
 [145] "13134"     "13164"     "13166"     "13206"     "13363"     "13382"    
 [151] "13383"     "13393"     "13404"     "13435"     "13487"     "13488"    
 [157] "13491"     "13492"     "13498"     "13524"     "13525"     "13526"    
 [163] "13529"     "13615"     "13617"     "13618"     "13649"     "13653"    
 [169] "13667"     "13731"     "13813"     "13819"     "13852"     "13854"    
 [175] "13856"     "13857"     "13866"     "13870"     "13874"     "13875"    
 [181] "13982"     "13983"     "13984"     "14008"     "14011"     "14087"    
 [187] "14088"     "14155"     "14160"     "14165"     "14178"     "14179"    
 [193] "14180"     "14183"     "14211"     "14228"     "14238"     "14276"    
 [199] "14283"     "14308"     "14309"     "14313"     "14366"     "14367"    
 [205] "14388"     "14421"     "14431"     "14453"     "14460"     "14461"    
 [211] "14462"     "14463"     "14531"     "14536"     "14566"     "14595"    
 [217] "14598"     "14610"     "14620"     "14622"     "14632"     "14633"    
 [223] "14654"     "14658"     "14682"     "14705"     "14714"     "14725"    
 [229] "14748"     "14764"     "14766"     "14782"     "14784"     "14810"    
 [235] "14815"     "14824"     "15013"     "15018"     "15078"     "15081"    
 [241] "15110"     "15194"     "15204"     "15205"     "15211"     "15212"    
 [247] "15213"     "15214"     "15221"     "15235"     "15251"     "15270"    
 [253] "15361"     "15364"     "15373"     "15375"     "15377"     "15378"    
 [259] "15387"     "15395"     "15396"     "15398"     "15405"     "15408"    
 [265] "15423"     "15430"     "15431"     "15433"     "15438"     "15446"    
 [271] "15463"     "15482"     "15484"     "15486"     "15487"     "15488"    
 [277] "15499"     "15500"     "15502"     "15511"     "15512"     "15516"    
 [283] "15567"     "15570"     "15574"     "15894"     "15904"     "16000"    
 [289] "16001"     "16002"     "16007"     "16011"     "16147"     "16153"    
 [295] "16157"     "16173"     "16175"     "16176"     "16322"     "16323"    
 [301] "16324"     "16330"     "16336"     "16337"     "16365"     "16401"    
 [307] "16410"     "16412"     "16433"     "16450"     "16477"     "16532"    
 [313] "16542"     "16590"     "16601"     "16650"     "16669"     "16691"    
 [319] "16777"     "16783"     "16842"     "16846"     "16847"     "16848"    
 [325] "16859"     "16866"     "16867"     "16869"     "16871"     "16872"    
 [331] "16875"     "16876"     "16878"     "16886"     "16952"     "16970"    
 [337] "16974"     "17125"     "17128"     "17129"     "17149"     "17171"    
 [343] "17173"     "17191"     "17221"     "17235"     "17240"     "17256"    
 [349] "17283"     "17289"     "17295"     "17300"     "17304"     "17311"    
 [355] "17319"     "17345"     "17350"     "17381"     "17390"     "17395"    
 [361] "17427"     "17450"     "17451"     "17535"     "17684"     "17685"    
 [367] "17686"     "17687"     "17688"     "17701"     "17702"     "17761"    
 [373] "17771"     "17776"     "17836"     "17864"     "17886"     "17977"    
 [379] "17978"     "17979"     "17986"     "18000"     "18004"     "18005"    
 [385] "18011"     "18014"     "18022"     "18072"     "18095"     "18119"    
 [391] "18121"     "18127"     "18128"     "18129"     "18142"     "18159"    
 [397] "18168"     "18194"     "18211"     "18285"     "18286"     "18291"    
 [403] "18292"     "18387"     "18413"     "18417"     "18426"     "18429"    
 [409] "18430"     "18431"     "18436"     "18441"     "18442"     "18472"    
 [415] "18475"     "18476"     "18504"     "18507"     "18514"     "18551"    
 [421] "18552"     "18555"     "18591"     "18595"     "18606"     "18617"    
 [427] "18667"     "18671"     "18747"     "18749"     "18763"     "18764"    
 [433] "18766"     "18775"     "18776"     "18783"     "18787"     "18791"    
 [439] "18792"     "18793"     "18795"     "18799"     "18802"     "18811"    
 [445] "18812"     "18814"     "18815"     "18817"     "18858"     "18861"    
 [451] "18952"     "19014"     "19015"     "19016"     "19049"     "19052"    
 [457] "19059"     "19090"     "19109"     "19110"     "19111"     "19112"    
 [463] "19113"     "19114"     "19116"     "19118"     "19119"     "19120"    
 [469] "19143"     "19156"     "19183"     "19204"     "19211"     "19214"    
 [475] "19215"     "19219"     "19223"     "19225"     "19229"     "19247"    
 [481] "19275"     "19288"     "19294"     "19317"     "19355"     "19357"    
 [487] "19359"     "19360"     "19361"     "19401"     "19411"     "19662"    
 [493] "19664"     "19701"     "19725"     "19733"     "19735"     "19773"    
 [499] "19821"     "19886"     "19891"     "20017"     "20104"     "20112"    
 [505] "20181"     "20182"     "20315"     "20317"     "20319"     "20346"    
 [511] "20363"     "20377"     "20397"     "20415"     "20423"     "20437"    
 [517] "20474"     "20475"     "20520"     "20541"     "20613"     "20655"    
 [523] "20662"     "20671"     "20674"     "20675"     "20681"     "20682"    
 [529] "20683"     "20686"     "20687"     "20690"     "20708"     "20719"    
 [535] "20720"     "20724"     "20729"     "20730"     "20732"     "20733"    
 [541] "20744"     "20758"     "20779"     "20826"     "20843"     "20848"    
 [547] "20850"     "20851"     "20860"     "20869"     "20871"     "20873"    
 [553] "20878"     "20892"     "20897"     "20899"     "20905"     "20910"    
 [559] "20957"     "20962"     "20997"     "21336"     "21357"     "21386"    
 [565] "21405"     "21410"     "21412"     "21414"     "21416"     "21425"    
 [571] "21454"     "21463"     "21674"     "21679"     "21744"     "21749"    
 [577] "21803"     "21808"     "21812"     "21821"     "21823"     "21824"    
 [583] "21830"     "21833"     "21834"     "21843"     "21849"     "21857"    
 [589] "21869"     "21887"     "21923"     "21945"     "21958"     "21959"    
 [595] "21973"     "21974"     "22022"     "22026"     "22061"     "22064"    
 [601] "22065"     "22068"     "22092"     "22113"     "22114"     "22115"    
 [607] "22127"     "22137"     "22174"     "22187"     "22209"     "22210"    
 [613] "22215"     "22329"     "22334"     "22337"     "22339"     "22353"    
 [619] "22371"     "22384"     "22412"     "22413"     "22415"     "22417"    
 [625] "22418"     "22421"     "22422"     "22431"     "22441"     "22445"    
 [631] "22446"     "22589"     "22632"     "22635"     "22661"     "22668"    
 [637] "22691"     "22694"     "22696"     "22697"     "22698"     "22701"    
 [643] "22702"     "22762"     "22764"     "22786"     "22787"     "22788"    
 [649] "22789"     "23793"     "23885"     "23920"     "23950"     "23967"    
 [655] "23968"     "23980"     "23991"     "23997"     "24061"     "24086"    
 [661] "24127"     "24128"     "26357"     "26362"     "26370"     "26380"    
 [667] "26384"     "26395"     "26407"     "26413"     "26416"     "26423"    
 [673] "26434"     "26437"     "26564"     "26909"     "26910"     "26927"    
 [679] "26934"     "26942"     "26946"     "26972"     "27061"     "27083"    
 [685] "27084"     "27206"     "27222"     "27354"     "27356"     "27372"    
 [691] "27386"     "28036"     "28078"     "28088"     "28105"     "28114"    
 [697] "28135"     "29871"     "29876"     "30054"     "30841"     "30939"    
 [703] "30953"     "30959"     "50500"     "50501"     "50505"     "50525"    
 [709] "50722"     "50785"     "50790"     "50796"     "50878"     "50915"    
 [715] "51792"     "51885"     "52020"     "52028"     "52679"     "52683"    
 [721] "52864"     "53381"     "53419"     "53422"     "53424"     "53601"    
 [727] "53604"     "53614"     "53814"     "53878"     "53885"     "53897"    
 [733] "53975"     "54003"     "54004"     "54137"     "54140"     "54204"    
 [739] "54383"     "54388"     "54418"     "54427"     "54486"     "54524"    
 [745] "54562"     "54608"     "54611"     "54650"     "54725"     "55925"    
 [751] "55978"     "55993"     "55994"     "56092"     "56094"     "56096"    
 [757] "56213"     "56218"     "56220"     "56223"     "56228"     "56274"    
 [763] "56291"     "56312"     "56334"     "56335"     "56371"     "56406"    
 [769] "56436"     "56449"     "56484"     "56503"     "56526"     "56635"    
 [775] "56693"     "56710"     "56711"     "56717"     "56739"     "56746"    
 [781] "57256"     "57264"     "57320"     "57746"     "57749"     "57815"    
 [787] "57816"     "57908"     "58186"     "58226"     "58230"     "58231"    
 [793] "58864"     "58991"     "58998"     "59030"     "59083"     "60530"    
 [799] "60534"     "60597"     "63872"     "64009"     "64335"     "64383"    
 [805] "64707"     "64931"     "65247"     "65971"     "66197"     "66313"    
 [811] "66392"     "66515"     "66573"     "66634"     "66654"     "66707"    
 [817] "66712"     "66713"     "66720"     "66722"     "66923"     "66977"    
 [823] "66983"     "67000"     "67010"     "67030"     "67042"     "67077"    
 [829] "67121"     "67141"     "67181"     "67204"     "67231"     "67310"    
 [835] "67331"     "67333"     "67345"     "67378"     "67402"     "67504"    
 [841] "67505"     "67555"     "67561"     "67652"     "67690"     "67713"    
 [847] "67753"     "67869"     "67909"     "67946"     "67968"     "67981"    
 [853] "68107"     "68166"     "68231"     "68265"     "68275"     "68298"    
 [859] "68328"     "68549"     "68708"     "68767"     "68911"     "68981"    
 [865] "69032"     "69064"     "69260"     "69286"     "69287"     "69307"    
 [871] "69310"     "69376"     "69444"     "69538"     "69546"     "69707"    
 [877] "69716"     "69852"     "69865"     "69928"     "69982"     "70069"    
 [883] "70093"     "70099"     "70235"     "70248"     "70375"     "70441"    
 [889] "70465"     "70503"     "70691"     "70772"     "70840"     "70862"    
 [895] "70873"     "70891"     "70956"     "70977"     "71062"     "71099"    
 [901] "71132"     "71175"     "71241"     "71242"     "71371"     "71567"    
 [907] "71709"     "71711"     "71765"     "71830"     "71836"     "71840"    
 [913] "71846"     "71854"     "71904"     "71914"     "71950"     "71981"    
 [919] "72135"     "72148"     "72162"     "72236"     "72415"     "72469"    
 [925] "72504"     "72508"     "72568"     "72634"     "72780"     "72787"    
 [931] "72891"     "72938"     "73242"     "73244"     "73296"     "73316"    
 [937] "73329"     "73336"     "73412"     "73456"     "73472"     "73542"    
 [943] "73673"     "73679"     "73721"     "74041"     "74068"     "74075"    
 [949] "74090"     "74117"     "74174"     "74188"     "74229"     "74237"    
 [955] "74267"     "74286"     "74288"     "74297"     "74309"     "74354"    
 [961] "74360"     "74369"     "74386"     "74401"     "74434"     "74446"    
 [967] "74450"     "74468"     "74469"     "74691"     "74716"     "74754"    
 [973] "74847"     "74927"     "75019"     "75033"     "75140"     "75178"    
 [979] "75202"     "75388"     "75410"     "75459"     "75469"     "75514"    
 [985] "75533"     "75571"     "75596"     "75605"     "75622"     "75642"    
 [991] "75646"     "75753"     "75801"     "75826"     "75828"     "75909"    
 [997] "76378"     "76400"     "76407"     "76486"     "76499"     "76718"    
[1003] "76800"     "76850"     "76856"     "76858"     "76867"     "76915"    
[1009] "76925"     "76943"     "77053"     "77128"     "77424"     "77595"    
[1015] "77684"     "77963"     "77980"     "78081"     "78124"     "78284"    
[1021] "78619"     "78634"     "78658"     "78784"     "78801"     "78803"    
[1027] "78925"     "80297"     "80517"     "80838"     "80884"     "80912"    
[1033] "81018"     "83456"     "83557"     "83558"     "83560"     "83561"    
[1039] "83964"     "83984"     "93684"     "93736"     "93757"     "93759"    
[1045] "93760"     "93837"     "93960"     "94221"     "94224"     "94244"    
[1051] "94246"     "97165"     "98558"     "98711"     "99412"     "99929"    
[1057] "100121"    "100155"    "100535"    "100986"    "101187"    "101476"   
[1063] "102774"    "103468"    "103554"    "103733"    "103768"    "104083"   
[1069] "104111"    "104148"    "104156"    "104263"    "104271"    "104310"   
[1075] "104362"    "104601"    "104799"    "104806"    "105349"    "105511"   
[1081] "105988"    "106389"    "106757"    "107515"    "107586"    "107626"   
[1087] "107656"    "107849"    "107970"    "107995"    "108829"    "108961"   
[1093] "109685"    "109689"    "109727"    "109785"    "110012"    "110084"   
[1099] "110147"    "110355"    "110459"    "110542"    "110957"    "110958"   
[1105] "112405"    "114606"    "114642"    "114661"    "114662"    "114714"   
[1111] "114875"    "140498"    "140557"    "170676"    "171285"    "171429"   
[1117] "171506"    "192119"    "192176"    "192195"    "192199"    "192897"   
[1123] "193838"    "194908"    "195434"    "207165"    "207304"    "207352"   
[1129] "207686"    "208169"    "208188"    "209091"    "210510"    "210529"   
[1135] "210554"    "211064"    "211484"    "211651"    "212517"    "212670"   
[1141] "212937"    "213081"    "213236"    "213272"    "213389"    "213541"   
[1147] "213742"    "214105"    "214253"    "214290"    "214292"    "214384"   
[1153] "214572"    "214575"    "214593"    "214901"    "215028"    "215029"   
[1159] "215095"    "215387"    "215854"    "216350"    "216725"    "216869"   
[1165] "217039"    "217116"    "217325"    "217715"    "217716"    "218214"   
[1171] "218454"    "218914"    "223593"    "223697"    "223825"    "223921"   
[1177] "223989"    "224045"    "224171"    "224661"    "224727"    "224826"   
[1183] "224902"    "225182"    "225865"    "226090"    "226162"    "226841"   
[1189] "227210"    "227394"    "227615"    "227631"    "227736"    "228421"   
[1195] "228980"    "229227"    "229357"    "229700"    "230103"    "230126"   
[1201] "230594"    "230809"    "230861"    "230899"    "231051"    "231633"   
[1207] "231672"    "231832"    "231912"    "232174"    "232223"    "232286"   
[1213] "232345"    "232664"    "233276"    "233328"    "234857"    "235072"   
[1219] "235320"    "235559"    "235626"    "235628"    "236266"    "236899"   
[1225] "237336"    "237625"    "237911"    "238055"    "238057"    "238247"   
[1231] "238328"    "238330"    "239083"    "239167"    "239528"    "239731"   
[1237] "240255"    "240590"    "240697"    "240725"    "240899"    "241624"   
[1243] "242202"    "242523"    "243862"    "243897"    "243905"    "244551"   
[1249] "245000"    "245865"    "246747"    "252828"    "252868"    "252967"   
[1255] "252973"    "259279"    "264134"    "268396"    "268420"    "268465"   
[1261] "268491"    "268591"    "268697"    "268755"    "268860"    "268903"   
[1267] "268930"    "269254"    "269275"    "269610"    "269682"    "270624"   
[1273] "271036"    "271127"    "271639"    "272643"    "276920"    "277353"   
[1279] "278240"    "280287"    "280667"    "280668"    "317653"    "319177"   
[1285] "319448"    "319953"    "320022"    "320244"    "320277"    "320558"   
[1291] "320752"    "320790"    "327826"    "328019"    "328365"    "328401"   
[1297] "328440"    "328580"    "328845"    "329557"    "329954"    "330149"   
[1303] "330188"    "330319"    "330409"    "330470"    "330830"    "330890"   
[1309] "331046"    "331416"    "332110"    "378430"    "378462"    "380654"   
[1315] "380684"    "380702"    "380709"    "380773"    "380855"    "380993"   
[1321] "380994"    "381022"    "381157"    "381196"    "381404"    "381489"   
[1327] "381677"    "381759"    "382077"    "382217"    "382275"    "382277"   
[1333] "382301"    "383491"    "384619"    "387139"    "387140"    "387153"   
[1339] "387156"    "387161"    "387162"    "387177"    "387178"    "387179"   
[1345] "387188"    "387198"    "387218"    "387244"    "387245"    "387246"   
[1351] "387247"    "399599"    "433700"    "434438"    "434784"    "434794"   
[1357] "442829"    "545156"    "546118"    "546272"    "546282"    "574428"   
[1363] "574437"    "574438"    "619517"    "619697"    "619991"    "622554"   
[1369] "625249"    "627081"    "629389"    "664799"    "664829"    "665187"   
[1375] "665270"    "665780"    "666317"    "666528"    "668110"    "668929"   
[1381] "671232"    "671564"    "723849"    "723868"    "723886"    "723932"   
[1387] "723939"    "723955"    "723956"    "723962"    "723965"    "723966"   
[1393] "735262"    "735309"    "751535"    "100009600" "100038417" "100038489"
[1399] "100038977" "100039030" "100039065" "100039120" "100039842" "100039905"
[1405] "100040054" "100040483" "100040608" "100040894" "100041897" "100042109"
[1411] "100042175" "100042922" "100042929" "100042931" "100042939" "100042943"
[1417] "100042944" "100042946" "100043216" "100048534" "100049545" "100049546"
[1423] "100049548" "100113365" "100124460" "100124479" "100124480" "100190765"
[1429] "100270744" "100504195" "100504642" "100861637" "100861665" "100861881"
[1435] "100862297" "101055773" "101056116" "101056210" "102443351" "102631559"
[1441] "102632183" "102633564" "102636501" "102638101" "102638793" "102639094"
[1447] "102639490" "102639895" "108168582"

$`GO:0000012`
 [1] "11545"  "14211"  "22064"  "22594"  "66408"  "70099"  "72103"  "93759" 
 [9] "104884" "319583"

> # output changes with annotation version !
> 
> y <- normDat.p[,1]
> names(y) <- featureNames(expressionSetGcrma)
> 
> y[1:10]
100009600    100012    100017    100019 100034251 100036521 100037258 100037278 
0.4328583 0.7448996 0.6088859 0.1845008 0.2312761 0.7865153 0.7772888 0.1037431 
100038570 100038635 
0.1368744 0.3272610 
> # 100009600    100012    100017    100019 100034251 100036521 100037258 100037278 
> # 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761 0.7865153 0.7772888 0.1037431 
> # 100038570 100038635 
> # 0.1368744 0.3272610 
> 
> mlpObject <- MLP(geneSet = goGeneSet, geneStatistic = y, minGenes = 5, maxGenes = 100, rowPermutations = TRUE, 
+     nPermutations = 6, smoothPValues = TRUE)
> 
> 
> 
> mlpObject[1:10, ]
           totalGeneSetSize testedGeneSetSize geneSetStatistic geneSetPValue
GO:0019886               14                14        1.0549211   0.001125601
GO:0060179                9                 8        1.2309410   0.001431926
GO:0002495               19                19        0.9388391   0.001718984
GO:0002478               24                24        0.8798107   0.001784424
GO:0002504               20                20        0.9113723   0.002124633
GO:0019884               30                28        0.8247444   0.003118940
GO:1901264               63                56        0.7076377   0.003575105
GO:0035088               44                39        0.7611007   0.003604597
GO:0061245               44                39        0.7611007   0.003604597
GO:0048002               67                44        0.7207161   0.005509354
                                                                                  geneSetDescription
GO:0019886         antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0060179                                                                      male mating behavior
GO:0002495                   antigen processing and presentation of peptide antigen via MHC class II
GO:0002478                          antigen processing and presentation of exogenous peptide antigen
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
GO:0019884                                  antigen processing and presentation of exogenous antigen
GO:1901264                                                         carbohydrate derivative transport
GO:0035088                                establishment or maintenance of apical/basal cell polarity
GO:0061245                                     establishment or maintenance of bipolar cell polarity
GO:0048002                                    antigen processing and presentation of peptide antigen
> # output changes with annotation version !
> 
> plotGOgraph(object = mlpObject, main = "test of main")
Loading required package: Rgraphviz
Loading required package: graph
Loading required package: grid

Attaching package: 'Rgraphviz'

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

    from, to

The following objects are masked from 'package:S4Vectors':

    from, to

Loading required package: GOstats
Loading required package: Category
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'GOstats'

The following object is masked from 'package:AnnotationDbi':

    makeGOGraph

Loading required package: annotate
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:graph':

    addNode


Attaching package: 'annotate'

The following object is masked from 'package:Rgraphviz':

    toFile

> 
> pdf(file = "test10.pdf", width = 10, height = 10)
> # x11(width = 10, height = 10)
> plot(mlpObject, nRow = 10) # by default:  type = "barplot"
> dev.off()
pdf 
  2 
> 
> unlink("test10.pdf")
> 
> if (FALSE){
+   pdf(file = "test5.pdf", width =10, height = 10)
+   mlpBarplot(object = mlpObject, geneSetSource = "GOBP", nRow = 10, descriptionLength = 5)
+   dev.off()
+   
+   unlink("test5.pdf")
+   
+   pdf(file = "test100.pdf", width =10, height = 20)
+   mlpBarplot(object = mlpObject, geneSetSource = "GOBP", nRow = 10, descriptionLength = 100)
+   dev.off()
+   
+   unlink("test100.pdf")
+ }
> 
> plot(mlpObject, type = "quantileCurves")
> plot(mlpObject, type = "GOgraph")
> 
> proc.time()
   user  system elapsed 
  38.75    3.53   42.71 

MLP.Rcheck/tests_x64/test.MLP.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.

> require(MLP)	
Loading required package: MLP
Loading required package: AnnotationDbi
Loading required package: stats4
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

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: affy
Loading required package: plotrix
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:plotrix':

    plotCI

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess

Loading required package: gmodels
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

The following object is masked from 'package:IRanges':

    trim

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    first, first<-

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    combine

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    combine

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    nobs

The following object is masked from 'package:stats':

    nobs

The following object is masked from 'package:utils':

    object.size

The following object is masked from 'package:base':

    startsWith

Loading required package: gtools
> set.seed(479)
> 
> # This is just the expressionset for this experiment.
> 
> pathExampleData <- system.file("exampleFiles", "expressionSetGcrma.rda", package = "MLP")
> load(pathExampleData)
> 
> # Libraries needed
> library(limma)

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

> library(org.Mm.eg.db) # for mouse

> 
> exprs(expressionSetGcrma)[1:2,]
              2760     2763     2765     2766     2768     2769     2761
100009600 2.371111 2.170060 2.233383 2.180717 2.325886 2.239441 2.297301
100012    2.176163 2.318876 2.419263 2.223307 2.585125 2.346060 2.292061
              2762    2764     2767     2770     2771
100009600 2.409001 2.49458 2.115814 2.371262 2.267459
100012    2.336415 2.47979 2.361981 2.330418 2.520918
> #              2760     2763     2765     2766     2768     2769     2761     2762    2764     2767
> #100009600 2.371111 2.170060 2.233383 2.180717 2.325886 2.239441 2.297301 2.409001 2.49458 2.115814
> #100012    2.176163 2.318876 2.419263 2.223307 2.585125 2.346060 2.292061 2.336415 2.47979 2.361981
> #              2770     2771
> #100009600 2.371262 2.267459
> #100012    2.330418 2.520918
> 
> pData(expressionSetGcrma)
     sample subGroup sampleColor subGroup1
2760      1        1     #FF0000        WT
2763      4        1     #FF0000        WT
2765      6        1     #FF0000        WT
2766      7        1     #FF0000        WT
2768      9        1     #FF0000        WT
2769     10        1     #FF0000        WT
2761      2        2     #0000FF        KO
2762      3        2     #0000FF        KO
2764      5        2     #0000FF        KO
2767      8        2     #0000FF        KO
2770     11        2     #0000FF        KO
2771     12        2     #0000FF        KO
> #     sample subGroup sampleColor
> #2760      1        1     #FF0000
> #2763      4        1     #FF0000
> #2765      6        1     #FF0000
> #2766      7        1     #FF0000
> #2768      9        1     #FF0000
> #2769     10        1     #FF0000
> #2761      2        2     #0000FF
> #2762      3        2     #0000FF
> #2764      5        2     #0000FF
> #2767      8        2     #0000FF
> #2770     11        2     #0000FF
> #2771     12        2     #0000FF
> 
> pData(expressionSetGcrma)$subGroup1 <- ifelse(pData(expressionSetGcrma)$subGroup==1,"WT","KO")
> 
> ###==============================================GENERATING LIMMA p-VALUES=================================
> 
> # boxplot(data.frame(exprs(expressionSetGcrma))
> normDat  <- normalizeQuantiles(exprs(expressionSetGcrma), ties=TRUE)
> subGroup <- pData(expressionSetGcrma)$subGroup
> design <- model.matrix(˜ -1 +factor(subGroup ))
> 
> colnames(design) <- c("group1", "group2")
> contrast.matrix <- makeContrasts(group1-group2, levels=design)
> fit <- lmFit(normDat,design)
> fit2 <- contrasts.fit(fit, contrast.matrix)
> fit2 <- eBayes(fit2)
> normDat.p <- fit2$p.value
> 
> normDat.p[1:5]
[1] 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761
> #[1] 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761
> 
> system.time(goGeneSet <- getGeneSets(species = "Mouse", geneSetSource = "GOBP", entrezIdentifiers = featureNames(expressionSetGcrma)))
Loading required package: GO.db

   user  system elapsed 
  24.86    0.90   25.76 
> goGeneSet[1:3]
$`GO:0000002`
 [1] "11545"  "16882"  "17258"  "17527"  "18975"  "19017"  "19819"  "22059" 
 [9] "23797"  "27393"  "27395"  "27397"  "50776"  "57813"  "66592"  "70556" 
[17] "72170"  "72962"  "74143"  "74244"  "74528"  "83408"  "83945"  "192287"
[25] "216021" "216805" "226153" "229524" "230784" "327762" "381760" "382985"
[33] "408022"

$`GO:0000003`
   [1] "11287"     "11352"     "11421"     "11430"     "11434"     "11441"    
   [7] "11477"     "11479"     "11480"     "11486"     "11495"     "11497"    
  [13] "11504"     "11516"     "11517"     "11535"     "11551"     "11552"    
  [19] "11553"     "11576"     "11600"     "11606"     "11614"     "11622"    
  [25] "11625"     "11647"     "11651"     "11674"     "11705"     "11757"    
  [31] "11789"     "11797"     "11804"     "11819"     "11820"     "11835"    
  [37] "11839"     "11857"     "11863"     "11865"     "11883"     "11920"    
  [43] "11998"     "12009"     "12018"     "12028"     "12034"     "12043"    
  [49] "12048"     "12050"     "12053"     "12124"     "12125"     "12142"    
  [55] "12144"     "12155"     "12159"     "12160"     "12161"     "12162"    
  [61] "12163"     "12164"     "12166"     "12167"     "12168"     "12173"    
  [67] "12190"     "12192"     "12211"     "12235"     "12236"     "12237"    
  [73] "12261"     "12305"     "12310"     "12316"     "12317"     "12323"    
  [79] "12344"     "12363"     "12366"     "12380"     "12387"     "12394"    
  [85] "12411"     "12416"     "12426"     "12427"     "12443"     "12447"    
  [91] "12448"     "12449"     "12458"     "12461"     "12462"     "12464"    
  [97] "12465"     "12466"     "12468"     "12469"     "12505"     "12527"    
 [103] "12530"     "12531"     "12532"     "12550"     "12566"     "12576"    
 [109] "12577"     "12589"     "12591"     "12592"     "12593"     "12606"    
 [115] "12608"     "12617"     "12638"     "12640"     "12659"     "12702"    
 [121] "12704"     "12705"     "12745"     "12753"     "12767"     "12801"    
 [127] "12804"     "12841"     "12846"     "12877"     "12916"     "12918"    
 [133] "12919"     "12946"     "12977"     "12981"     "13006"     "13030"    
 [139] "13039"     "13046"     "13052"     "13070"     "13075"     "13123"    
 [145] "13134"     "13164"     "13166"     "13206"     "13363"     "13382"    
 [151] "13383"     "13393"     "13404"     "13435"     "13487"     "13488"    
 [157] "13491"     "13492"     "13498"     "13524"     "13525"     "13526"    
 [163] "13529"     "13615"     "13617"     "13618"     "13649"     "13653"    
 [169] "13667"     "13731"     "13813"     "13819"     "13852"     "13854"    
 [175] "13856"     "13857"     "13866"     "13870"     "13874"     "13875"    
 [181] "13982"     "13983"     "13984"     "14008"     "14011"     "14087"    
 [187] "14088"     "14155"     "14160"     "14165"     "14178"     "14179"    
 [193] "14180"     "14183"     "14211"     "14228"     "14238"     "14276"    
 [199] "14283"     "14308"     "14309"     "14313"     "14366"     "14367"    
 [205] "14388"     "14421"     "14431"     "14453"     "14460"     "14461"    
 [211] "14462"     "14463"     "14531"     "14536"     "14566"     "14595"    
 [217] "14598"     "14610"     "14620"     "14622"     "14632"     "14633"    
 [223] "14654"     "14658"     "14682"     "14705"     "14714"     "14725"    
 [229] "14748"     "14764"     "14766"     "14782"     "14784"     "14810"    
 [235] "14815"     "14824"     "15013"     "15018"     "15078"     "15081"    
 [241] "15110"     "15194"     "15204"     "15205"     "15211"     "15212"    
 [247] "15213"     "15214"     "15221"     "15235"     "15251"     "15270"    
 [253] "15361"     "15364"     "15373"     "15375"     "15377"     "15378"    
 [259] "15387"     "15395"     "15396"     "15398"     "15405"     "15408"    
 [265] "15423"     "15430"     "15431"     "15433"     "15438"     "15446"    
 [271] "15463"     "15482"     "15484"     "15486"     "15487"     "15488"    
 [277] "15499"     "15500"     "15502"     "15511"     "15512"     "15516"    
 [283] "15567"     "15570"     "15574"     "15894"     "15904"     "16000"    
 [289] "16001"     "16002"     "16007"     "16011"     "16147"     "16153"    
 [295] "16157"     "16173"     "16175"     "16176"     "16322"     "16323"    
 [301] "16324"     "16330"     "16336"     "16337"     "16365"     "16401"    
 [307] "16410"     "16412"     "16433"     "16450"     "16477"     "16532"    
 [313] "16542"     "16590"     "16601"     "16650"     "16669"     "16691"    
 [319] "16777"     "16783"     "16842"     "16846"     "16847"     "16848"    
 [325] "16859"     "16866"     "16867"     "16869"     "16871"     "16872"    
 [331] "16875"     "16876"     "16878"     "16886"     "16952"     "16970"    
 [337] "16974"     "17125"     "17128"     "17129"     "17149"     "17171"    
 [343] "17173"     "17191"     "17221"     "17235"     "17240"     "17256"    
 [349] "17283"     "17289"     "17295"     "17300"     "17304"     "17311"    
 [355] "17319"     "17345"     "17350"     "17381"     "17390"     "17395"    
 [361] "17427"     "17450"     "17451"     "17535"     "17684"     "17685"    
 [367] "17686"     "17687"     "17688"     "17701"     "17702"     "17761"    
 [373] "17771"     "17776"     "17836"     "17864"     "17886"     "17977"    
 [379] "17978"     "17979"     "17986"     "18000"     "18004"     "18005"    
 [385] "18011"     "18014"     "18022"     "18072"     "18095"     "18119"    
 [391] "18121"     "18127"     "18128"     "18129"     "18142"     "18159"    
 [397] "18168"     "18194"     "18211"     "18285"     "18286"     "18291"    
 [403] "18292"     "18387"     "18413"     "18417"     "18426"     "18429"    
 [409] "18430"     "18431"     "18436"     "18441"     "18442"     "18472"    
 [415] "18475"     "18476"     "18504"     "18507"     "18514"     "18551"    
 [421] "18552"     "18555"     "18591"     "18595"     "18606"     "18617"    
 [427] "18667"     "18671"     "18747"     "18749"     "18763"     "18764"    
 [433] "18766"     "18775"     "18776"     "18783"     "18787"     "18791"    
 [439] "18792"     "18793"     "18795"     "18799"     "18802"     "18811"    
 [445] "18812"     "18814"     "18815"     "18817"     "18858"     "18861"    
 [451] "18952"     "19014"     "19015"     "19016"     "19049"     "19052"    
 [457] "19059"     "19090"     "19109"     "19110"     "19111"     "19112"    
 [463] "19113"     "19114"     "19116"     "19118"     "19119"     "19120"    
 [469] "19143"     "19156"     "19183"     "19204"     "19211"     "19214"    
 [475] "19215"     "19219"     "19223"     "19225"     "19229"     "19247"    
 [481] "19275"     "19288"     "19294"     "19317"     "19355"     "19357"    
 [487] "19359"     "19360"     "19361"     "19401"     "19411"     "19662"    
 [493] "19664"     "19701"     "19725"     "19733"     "19735"     "19773"    
 [499] "19821"     "19886"     "19891"     "20017"     "20104"     "20112"    
 [505] "20181"     "20182"     "20315"     "20317"     "20319"     "20346"    
 [511] "20363"     "20377"     "20397"     "20415"     "20423"     "20437"    
 [517] "20474"     "20475"     "20520"     "20541"     "20613"     "20655"    
 [523] "20662"     "20671"     "20674"     "20675"     "20681"     "20682"    
 [529] "20683"     "20686"     "20687"     "20690"     "20708"     "20719"    
 [535] "20720"     "20724"     "20729"     "20730"     "20732"     "20733"    
 [541] "20744"     "20758"     "20779"     "20826"     "20843"     "20848"    
 [547] "20850"     "20851"     "20860"     "20869"     "20871"     "20873"    
 [553] "20878"     "20892"     "20897"     "20899"     "20905"     "20910"    
 [559] "20957"     "20962"     "20997"     "21336"     "21357"     "21386"    
 [565] "21405"     "21410"     "21412"     "21414"     "21416"     "21425"    
 [571] "21454"     "21463"     "21674"     "21679"     "21744"     "21749"    
 [577] "21803"     "21808"     "21812"     "21821"     "21823"     "21824"    
 [583] "21830"     "21833"     "21834"     "21843"     "21849"     "21857"    
 [589] "21869"     "21887"     "21923"     "21945"     "21958"     "21959"    
 [595] "21973"     "21974"     "22022"     "22026"     "22061"     "22064"    
 [601] "22065"     "22068"     "22092"     "22113"     "22114"     "22115"    
 [607] "22127"     "22137"     "22174"     "22187"     "22209"     "22210"    
 [613] "22215"     "22329"     "22334"     "22337"     "22339"     "22353"    
 [619] "22371"     "22384"     "22412"     "22413"     "22415"     "22417"    
 [625] "22418"     "22421"     "22422"     "22431"     "22441"     "22445"    
 [631] "22446"     "22589"     "22632"     "22635"     "22661"     "22668"    
 [637] "22691"     "22694"     "22696"     "22697"     "22698"     "22701"    
 [643] "22702"     "22762"     "22764"     "22786"     "22787"     "22788"    
 [649] "22789"     "23793"     "23885"     "23920"     "23950"     "23967"    
 [655] "23968"     "23980"     "23991"     "23997"     "24061"     "24086"    
 [661] "24127"     "24128"     "26357"     "26362"     "26370"     "26380"    
 [667] "26384"     "26395"     "26407"     "26413"     "26416"     "26423"    
 [673] "26434"     "26437"     "26564"     "26909"     "26910"     "26927"    
 [679] "26934"     "26942"     "26946"     "26972"     "27061"     "27083"    
 [685] "27084"     "27206"     "27222"     "27354"     "27356"     "27372"    
 [691] "27386"     "28036"     "28078"     "28088"     "28105"     "28114"    
 [697] "28135"     "29871"     "29876"     "30054"     "30841"     "30939"    
 [703] "30953"     "30959"     "50500"     "50501"     "50505"     "50525"    
 [709] "50722"     "50785"     "50790"     "50796"     "50878"     "50915"    
 [715] "51792"     "51885"     "52020"     "52028"     "52679"     "52683"    
 [721] "52864"     "53381"     "53419"     "53422"     "53424"     "53601"    
 [727] "53604"     "53614"     "53814"     "53878"     "53885"     "53897"    
 [733] "53975"     "54003"     "54004"     "54137"     "54140"     "54204"    
 [739] "54383"     "54388"     "54418"     "54427"     "54486"     "54524"    
 [745] "54562"     "54608"     "54611"     "54650"     "54725"     "55925"    
 [751] "55978"     "55993"     "55994"     "56092"     "56094"     "56096"    
 [757] "56213"     "56218"     "56220"     "56223"     "56228"     "56274"    
 [763] "56291"     "56312"     "56334"     "56335"     "56371"     "56406"    
 [769] "56436"     "56449"     "56484"     "56503"     "56526"     "56635"    
 [775] "56693"     "56710"     "56711"     "56717"     "56739"     "56746"    
 [781] "57256"     "57264"     "57320"     "57746"     "57749"     "57815"    
 [787] "57816"     "57908"     "58186"     "58226"     "58230"     "58231"    
 [793] "58864"     "58991"     "58998"     "59030"     "59083"     "60530"    
 [799] "60534"     "60597"     "63872"     "64009"     "64335"     "64383"    
 [805] "64707"     "64931"     "65247"     "65971"     "66197"     "66313"    
 [811] "66392"     "66515"     "66573"     "66634"     "66654"     "66707"    
 [817] "66712"     "66713"     "66720"     "66722"     "66923"     "66977"    
 [823] "66983"     "67000"     "67010"     "67030"     "67042"     "67077"    
 [829] "67121"     "67141"     "67181"     "67204"     "67231"     "67310"    
 [835] "67331"     "67333"     "67345"     "67378"     "67402"     "67504"    
 [841] "67505"     "67555"     "67561"     "67652"     "67690"     "67713"    
 [847] "67753"     "67869"     "67909"     "67946"     "67968"     "67981"    
 [853] "68107"     "68166"     "68231"     "68265"     "68275"     "68298"    
 [859] "68328"     "68549"     "68708"     "68767"     "68911"     "68981"    
 [865] "69032"     "69064"     "69260"     "69286"     "69287"     "69307"    
 [871] "69310"     "69376"     "69444"     "69538"     "69546"     "69707"    
 [877] "69716"     "69852"     "69865"     "69928"     "69982"     "70069"    
 [883] "70093"     "70099"     "70235"     "70248"     "70375"     "70441"    
 [889] "70465"     "70503"     "70691"     "70772"     "70840"     "70862"    
 [895] "70873"     "70891"     "70956"     "70977"     "71062"     "71099"    
 [901] "71132"     "71175"     "71241"     "71242"     "71371"     "71567"    
 [907] "71709"     "71711"     "71765"     "71830"     "71836"     "71840"    
 [913] "71846"     "71854"     "71904"     "71914"     "71950"     "71981"    
 [919] "72135"     "72148"     "72162"     "72236"     "72415"     "72469"    
 [925] "72504"     "72508"     "72568"     "72634"     "72780"     "72787"    
 [931] "72891"     "72938"     "73242"     "73244"     "73296"     "73316"    
 [937] "73329"     "73336"     "73412"     "73456"     "73472"     "73542"    
 [943] "73673"     "73679"     "73721"     "74041"     "74068"     "74075"    
 [949] "74090"     "74117"     "74174"     "74188"     "74229"     "74237"    
 [955] "74267"     "74286"     "74288"     "74297"     "74309"     "74354"    
 [961] "74360"     "74369"     "74386"     "74401"     "74434"     "74446"    
 [967] "74450"     "74468"     "74469"     "74691"     "74716"     "74754"    
 [973] "74847"     "74927"     "75019"     "75033"     "75140"     "75178"    
 [979] "75202"     "75388"     "75410"     "75459"     "75469"     "75514"    
 [985] "75533"     "75571"     "75596"     "75605"     "75622"     "75642"    
 [991] "75646"     "75753"     "75801"     "75826"     "75828"     "75909"    
 [997] "76378"     "76400"     "76407"     "76486"     "76499"     "76718"    
[1003] "76800"     "76850"     "76856"     "76858"     "76867"     "76915"    
[1009] "76925"     "76943"     "77053"     "77128"     "77424"     "77595"    
[1015] "77684"     "77963"     "77980"     "78081"     "78124"     "78284"    
[1021] "78619"     "78634"     "78658"     "78784"     "78801"     "78803"    
[1027] "78925"     "80297"     "80517"     "80838"     "80884"     "80912"    
[1033] "81018"     "83456"     "83557"     "83558"     "83560"     "83561"    
[1039] "83964"     "83984"     "93684"     "93736"     "93757"     "93759"    
[1045] "93760"     "93837"     "93960"     "94221"     "94224"     "94244"    
[1051] "94246"     "97165"     "98558"     "98711"     "99412"     "99929"    
[1057] "100121"    "100155"    "100535"    "100986"    "101187"    "101476"   
[1063] "102774"    "103468"    "103554"    "103733"    "103768"    "104083"   
[1069] "104111"    "104148"    "104156"    "104263"    "104271"    "104310"   
[1075] "104362"    "104601"    "104799"    "104806"    "105349"    "105511"   
[1081] "105988"    "106389"    "106757"    "107515"    "107586"    "107626"   
[1087] "107656"    "107849"    "107970"    "107995"    "108829"    "108961"   
[1093] "109685"    "109689"    "109727"    "109785"    "110012"    "110084"   
[1099] "110147"    "110355"    "110459"    "110542"    "110957"    "110958"   
[1105] "112405"    "114606"    "114642"    "114661"    "114662"    "114714"   
[1111] "114875"    "140498"    "140557"    "170676"    "171285"    "171429"   
[1117] "171506"    "192119"    "192176"    "192195"    "192199"    "192897"   
[1123] "193838"    "194908"    "195434"    "207165"    "207304"    "207352"   
[1129] "207686"    "208169"    "208188"    "209091"    "210510"    "210529"   
[1135] "210554"    "211064"    "211484"    "211651"    "212517"    "212670"   
[1141] "212937"    "213081"    "213236"    "213272"    "213389"    "213541"   
[1147] "213742"    "214105"    "214253"    "214290"    "214292"    "214384"   
[1153] "214572"    "214575"    "214593"    "214901"    "215028"    "215029"   
[1159] "215095"    "215387"    "215854"    "216350"    "216725"    "216869"   
[1165] "217039"    "217116"    "217325"    "217715"    "217716"    "218214"   
[1171] "218454"    "218914"    "223593"    "223697"    "223825"    "223921"   
[1177] "223989"    "224045"    "224171"    "224661"    "224727"    "224826"   
[1183] "224902"    "225182"    "225865"    "226090"    "226162"    "226841"   
[1189] "227210"    "227394"    "227615"    "227631"    "227736"    "228421"   
[1195] "228980"    "229227"    "229357"    "229700"    "230103"    "230126"   
[1201] "230594"    "230809"    "230861"    "230899"    "231051"    "231633"   
[1207] "231672"    "231832"    "231912"    "232174"    "232223"    "232286"   
[1213] "232345"    "232664"    "233276"    "233328"    "234857"    "235072"   
[1219] "235320"    "235559"    "235626"    "235628"    "236266"    "236899"   
[1225] "237336"    "237625"    "237911"    "238055"    "238057"    "238247"   
[1231] "238328"    "238330"    "239083"    "239167"    "239528"    "239731"   
[1237] "240255"    "240590"    "240697"    "240725"    "240899"    "241624"   
[1243] "242202"    "242523"    "243862"    "243897"    "243905"    "244551"   
[1249] "245000"    "245865"    "246747"    "252828"    "252868"    "252967"   
[1255] "252973"    "259279"    "264134"    "268396"    "268420"    "268465"   
[1261] "268491"    "268591"    "268697"    "268755"    "268860"    "268903"   
[1267] "268930"    "269254"    "269275"    "269610"    "269682"    "270624"   
[1273] "271036"    "271127"    "271639"    "272643"    "276920"    "277353"   
[1279] "278240"    "280287"    "280667"    "280668"    "317653"    "319177"   
[1285] "319448"    "319953"    "320022"    "320244"    "320277"    "320558"   
[1291] "320752"    "320790"    "327826"    "328019"    "328365"    "328401"   
[1297] "328440"    "328580"    "328845"    "329557"    "329954"    "330149"   
[1303] "330188"    "330319"    "330409"    "330470"    "330830"    "330890"   
[1309] "331046"    "331416"    "332110"    "378430"    "378462"    "380654"   
[1315] "380684"    "380702"    "380709"    "380773"    "380855"    "380993"   
[1321] "380994"    "381022"    "381157"    "381196"    "381404"    "381489"   
[1327] "381677"    "381759"    "382077"    "382217"    "382275"    "382277"   
[1333] "382301"    "383491"    "384619"    "387139"    "387140"    "387153"   
[1339] "387156"    "387161"    "387162"    "387177"    "387178"    "387179"   
[1345] "387188"    "387198"    "387218"    "387244"    "387245"    "387246"   
[1351] "387247"    "399599"    "433700"    "434438"    "434784"    "434794"   
[1357] "442829"    "545156"    "546118"    "546272"    "546282"    "574428"   
[1363] "574437"    "574438"    "619517"    "619697"    "619991"    "622554"   
[1369] "625249"    "627081"    "629389"    "664799"    "664829"    "665187"   
[1375] "665270"    "665780"    "666317"    "666528"    "668110"    "668929"   
[1381] "671232"    "671564"    "723849"    "723868"    "723886"    "723932"   
[1387] "723939"    "723955"    "723956"    "723962"    "723965"    "723966"   
[1393] "735262"    "735309"    "751535"    "100009600" "100038417" "100038489"
[1399] "100038977" "100039030" "100039065" "100039120" "100039842" "100039905"
[1405] "100040054" "100040483" "100040608" "100040894" "100041897" "100042109"
[1411] "100042175" "100042922" "100042929" "100042931" "100042939" "100042943"
[1417] "100042944" "100042946" "100043216" "100048534" "100049545" "100049546"
[1423] "100049548" "100113365" "100124460" "100124479" "100124480" "100190765"
[1429] "100270744" "100504195" "100504642" "100861637" "100861665" "100861881"
[1435] "100862297" "101055773" "101056116" "101056210" "102443351" "102631559"
[1441] "102632183" "102633564" "102636501" "102638101" "102638793" "102639094"
[1447] "102639490" "102639895" "108168582"

$`GO:0000012`
 [1] "11545"  "14211"  "22064"  "22594"  "66408"  "70099"  "72103"  "93759" 
 [9] "104884" "319583"

> # output changes with annotation version !
> 
> y <- normDat.p[,1]
> names(y) <- featureNames(expressionSetGcrma)
> 
> y[1:10]
100009600    100012    100017    100019 100034251 100036521 100037258 100037278 
0.4328583 0.7448996 0.6088859 0.1845008 0.2312761 0.7865153 0.7772888 0.1037431 
100038570 100038635 
0.1368744 0.3272610 
> # 100009600    100012    100017    100019 100034251 100036521 100037258 100037278 
> # 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761 0.7865153 0.7772888 0.1037431 
> # 100038570 100038635 
> # 0.1368744 0.3272610 
> 
> mlpObject <- MLP(geneSet = goGeneSet, geneStatistic = y, minGenes = 5, maxGenes = 100, rowPermutations = TRUE, 
+     nPermutations = 6, smoothPValues = TRUE)
> 
> 
> 
> mlpObject[1:10, ]
           totalGeneSetSize testedGeneSetSize geneSetStatistic geneSetPValue
GO:0019886               14                14        1.0549211   0.001125601
GO:0060179                9                 8        1.2309410   0.001431926
GO:0002495               19                19        0.9388391   0.001718984
GO:0002478               24                24        0.8798107   0.001784424
GO:0002504               20                20        0.9113723   0.002124633
GO:0019884               30                28        0.8247444   0.003118940
GO:1901264               63                56        0.7076377   0.003575105
GO:0035088               44                39        0.7611007   0.003604597
GO:0061245               44                39        0.7611007   0.003604597
GO:0048002               67                44        0.7207161   0.005509354
                                                                                  geneSetDescription
GO:0019886         antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0060179                                                                      male mating behavior
GO:0002495                   antigen processing and presentation of peptide antigen via MHC class II
GO:0002478                          antigen processing and presentation of exogenous peptide antigen
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
GO:0019884                                  antigen processing and presentation of exogenous antigen
GO:1901264                                                         carbohydrate derivative transport
GO:0035088                                establishment or maintenance of apical/basal cell polarity
GO:0061245                                     establishment or maintenance of bipolar cell polarity
GO:0048002                                    antigen processing and presentation of peptide antigen
> # output changes with annotation version !
> 
> plotGOgraph(object = mlpObject, main = "test of main")
Loading required package: Rgraphviz
Loading required package: graph
Loading required package: grid

Attaching package: 'Rgraphviz'

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

    from, to

The following objects are masked from 'package:S4Vectors':

    from, to

Loading required package: GOstats
Loading required package: Category
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'GOstats'

The following object is masked from 'package:AnnotationDbi':

    makeGOGraph

Loading required package: annotate
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:graph':

    addNode


Attaching package: 'annotate'

The following object is masked from 'package:Rgraphviz':

    toFile

> 
> pdf(file = "test10.pdf", width = 10, height = 10)
> # x11(width = 10, height = 10)
> plot(mlpObject, nRow = 10) # by default:  type = "barplot"
> dev.off()
pdf 
  2 
> 
> unlink("test10.pdf")
> 
> if (FALSE){
+   pdf(file = "test5.pdf", width =10, height = 10)
+   mlpBarplot(object = mlpObject, geneSetSource = "GOBP", nRow = 10, descriptionLength = 5)
+   dev.off()
+   
+   unlink("test5.pdf")
+   
+   pdf(file = "test100.pdf", width =10, height = 20)
+   mlpBarplot(object = mlpObject, geneSetSource = "GOBP", nRow = 10, descriptionLength = 100)
+   dev.off()
+   
+   unlink("test100.pdf")
+ }
> 
> plot(mlpObject, type = "quantileCurves")
> plot(mlpObject, type = "GOgraph")
> 
> proc.time()
   user  system elapsed 
  44.42    1.15   45.98 

Example timings

MLP.Rcheck/examples_i386/MLP-Ex.timings

nameusersystemelapsed
MLP18.78 0.8019.80
getGeneSets 18.31 3.67105.55
mlpBarplot0.060.020.14
plot.MLP3.110.033.14
plotGOgraph0.670.050.72
plotGeneSetSignificance0.720.011.50

MLP.Rcheck/examples_x64/MLP-Ex.timings

nameusersystemelapsed
MLP19.59 0.7020.30
getGeneSets19.84 0.9720.81
mlpBarplot0.080.000.08
plot.MLP2.720.032.75
plotGOgraph0.660.020.68
plotGeneSetSignificance0.650.020.76