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This page was generated on 2021-10-15 15:06:12 -0400 (Fri, 15 Oct 2021).

CHECK results for MLP on tokay2

To the developers/maintainers of the MLP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MLP.git to
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raw results

Package 1163/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MLP 1.40.0  (landing page)
Tobias Verbeke
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/MLP
git_branch: RELEASE_3_13
git_last_commit: 40d425d
git_last_commit_date: 2021-05-19 11:46:51 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MLP
Version: 1.40.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MLP_1.40.0.tar.gz
StartedAt: 2021-10-15 02:06:59 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 02:20:24 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 805.0 seconds
RetCode: 0
Status:   OK  
CheckDir: MLP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MLP_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MLP.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.40.0'
* 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 whether package 'MLP' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 (user + system) or elapsed time > 5s
                       user system elapsed
getGeneSets           66.53   5.06   94.42
addGeneSetDescription 55.43   4.33   59.76
MLP                   22.32   1.65   24.08
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
getGeneSets           68.08   0.78   89.58
addGeneSetDescription 52.05   1.15   53.22
MLP                   20.67   0.33   21.00
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.KEGG.R'
  Running 'test.MLP.R'
 OK
** running tests for arch 'x64' ...
  Running 'test.KEGG.R'
  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: OK


Installation output

MLP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MLP_1.40.0.tar.gz && rm -rf MLP.buildbin-libdir && mkdir MLP.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MLP.buildbin-libdir MLP_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MLP_1.40.0.zip && rm MLP_1.40.0.tar.gz MLP_1.40.0.zip
###
##############################################################################
##############################################################################


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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  7 4108k    7  306k    0     0   838k      0  0:00:04 --:--:--  0:00:04  838k
 53 4108k   53 2177k    0     0  1580k      0  0:00:02  0:00:01  0:00:01 1580k
100 4108k  100 4108k    0     0  1894k      0  0:00:02  0:00:02 --:--:-- 1895k

install for i386

* installing *source* package 'MLP' ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'MLP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MLP' as MLP_1.40.0.zip
* DONE (MLP)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MLP' successfully unpacked and MD5 sums checked

Tests output

MLP.Rcheck/tests_i386/test.KEGG.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> library(MLP)
> 
> pathPValues <- system.file("exampleFiles", "examplePValues.rda", package = "MLP")
> load(pathPValues)
> 
> pvalues <- examplePValues[seq.int(1000)]
> 
> system.time(geneSet <- getGeneSets(
+ 	species = "Mouse", 
+ 	geneSetSource = "KEGG", 
+ 	entrezIdentifiers = names(pvalues)
+ ))
   user  system elapsed 
  51.12    1.09   74.09 
> 
> set.seed(111)
> mlpOut <- MLP(
+ 	geneSet = geneSet, 
+ 	geneStatistic = pvalues
+ ) 	
> 
> mlpOutWithGeneSetDescr <- addGeneSetDescription(object = mlpOut, geneSetSource = "KEGG")
Warning message:
In addGeneSetDescription(object = mlpOut, geneSetSource = "KEGG") :
  The MLP object already contains a column 'geneSetDescription'
> 
> 	
> 
> proc.time()
   user  system elapsed 
  58.39    2.03  107.96 

MLP.Rcheck/tests_x64/test.KEGG.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> library(MLP)
> 
> pathPValues <- system.file("exampleFiles", "examplePValues.rda", package = "MLP")
> load(pathPValues)
> 
> pvalues <- examplePValues[seq.int(1000)]
> 
> system.time(geneSet <- getGeneSets(
+ 	species = "Mouse", 
+ 	geneSetSource = "KEGG", 
+ 	entrezIdentifiers = names(pvalues)
+ ))
   user  system elapsed 
  50.71    0.73   72.58 
> 
> set.seed(111)
> mlpOut <- MLP(
+ 	geneSet = geneSet, 
+ 	geneStatistic = pvalues
+ ) 	
> 
> mlpOutWithGeneSetDescr <- addGeneSetDescription(object = mlpOut, geneSetSource = "KEGG")
Warning message:
In addGeneSetDescription(object = mlpOut, geneSetSource = "KEGG") :
  The MLP object already contains a column 'geneSetDescription'
> 
> 	
> 
> proc.time()
   user  system elapsed 
  56.64    1.65  104.92 

MLP.Rcheck/tests_i386/test.MLP.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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
> 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)
> library(org.Mm.eg.db) # for mouse
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 object is masked from 'package:limma':

    plotMA

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

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 objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows


> 
> 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 namespace: GO.db

   user  system elapsed 
  26.05    3.39   29.44 
> goGeneSet[1:3]
$`GO:0000002`
 [1] "11545"  "12628"  "16882"  "17258"  "17527"  "19017"  "21975"  "22059" 
 [9] "23797"  "27393"  "27395"  "27397"  "50776"  "57813"  "70556"  "72170" 
[17] "72962"  "74143"  "74528"  "83408"  "192287" "216021" "216805" "230784"
[25] "327762" "408022"

$`GO:0000003`
   [1] "11287"     "11352"     "11421"     "11430"     "11434"     "11441"    
   [7] "11477"     "11479"     "11480"     "11486"     "11495"     "11497"    
  [13] "11498"     "11499"     "11504"     "11516"     "11517"     "11535"    
  [19] "11551"     "11552"     "11553"     "11576"     "11600"     "11606"    
  [25] "11614"     "11622"     "11625"     "11643"     "11647"     "11651"    
  [31] "11674"     "11705"     "11747"     "11757"     "11774"     "11789"    
  [37] "11797"     "11804"     "11819"     "11820"     "11835"     "11839"    
  [43] "11857"     "11863"     "11865"     "11883"     "11920"     "11998"    
  [49] "12009"     "12018"     "12028"     "12034"     "12041"     "12043"    
  [55] "12048"     "12050"     "12053"     "12124"     "12125"     "12142"    
  [61] "12155"     "12159"     "12160"     "12161"     "12162"     "12163"    
  [67] "12164"     "12166"     "12167"     "12168"     "12173"     "12190"    
  [73] "12192"     "12211"     "12215"     "12235"     "12236"     "12237"    
  [79] "12261"     "12266"     "12290"     "12305"     "12310"     "12316"    
  [85] "12317"     "12323"     "12344"     "12363"     "12366"     "12380"    
  [91] "12387"     "12394"     "12411"     "12416"     "12426"     "12427"    
  [97] "12442"     "12443"     "12447"     "12448"     "12449"     "12458"    
 [103] "12461"     "12462"     "12464"     "12465"     "12466"     "12468"    
 [109] "12469"     "12505"     "12527"     "12530"     "12531"     "12532"    
 [115] "12550"     "12566"     "12576"     "12577"     "12589"     "12591"    
 [121] "12592"     "12593"     "12606"     "12608"     "12617"     "12638"    
 [127] "12640"     "12659"     "12702"     "12704"     "12705"     "12745"    
 [133] "12753"     "12767"     "12801"     "12804"     "12841"     "12846"    
 [139] "12877"     "12916"     "12918"     "12919"     "12929"     "12946"    
 [145] "12977"     "12981"     "13006"     "13030"     "13039"     "13046"    
 [151] "13052"     "13070"     "13075"     "13123"     "13134"     "13164"    
 [157] "13166"     "13205"     "13206"     "13363"     "13382"     "13383"    
 [163] "13393"     "13404"     "13411"     "13435"     "13487"     "13488"    
 [169] "13491"     "13492"     "13498"     "13524"     "13525"     "13526"    
 [175] "13529"     "13615"     "13617"     "13618"     "13649"     "13653"    
 [181] "13667"     "13731"     "13813"     "13819"     "13852"     "13854"    
 [187] "13856"     "13857"     "13866"     "13870"     "13874"     "13875"    
 [193] "13982"     "13983"     "13984"     "14008"     "14011"     "14087"    
 [199] "14088"     "14155"     "14160"     "14165"     "14178"     "14179"    
 [205] "14180"     "14183"     "14211"     "14228"     "14238"     "14275"    
 [211] "14276"     "14283"     "14308"     "14309"     "14313"     "14347"    
 [217] "14366"     "14367"     "14388"     "14402"     "14421"     "14431"    
 [223] "14447"     "14453"     "14460"     "14461"     "14462"     "14463"    
 [229] "14531"     "14536"     "14566"     "14595"     "14598"     "14609"    
 [235] "14610"     "14620"     "14622"     "14632"     "14633"     "14654"    
 [241] "14658"     "14682"     "14705"     "14714"     "14725"     "14748"    
 [247] "14764"     "14766"     "14782"     "14784"     "14810"     "14815"    
 [253] "14824"     "15013"     "15018"     "15078"     "15081"     "15110"    
 [259] "15170"     "15182"     "15194"     "15204"     "15205"     "15209"    
 [265] "15211"     "15212"     "15213"     "15214"     "15221"     "15235"    
 [271] "15247"     "15251"     "15270"     "15361"     "15364"     "15373"    
 [277] "15375"     "15377"     "15378"     "15387"     "15395"     "15396"    
 [283] "15398"     "15405"     "15408"     "15423"     "15430"     "15431"    
 [289] "15433"     "15438"     "15446"     "15463"     "15482"     "15484"    
 [295] "15486"     "15487"     "15488"     "15499"     "15500"     "15502"    
 [301] "15511"     "15512"     "15516"     "15567"     "15570"     "15574"    
 [307] "15894"     "15904"     "16000"     "16001"     "16002"     "16007"    
 [313] "16011"     "16147"     "16153"     "16157"     "16173"     "16175"    
 [319] "16176"     "16319"     "16322"     "16323"     "16324"     "16330"    
 [325] "16336"     "16337"     "16365"     "16401"     "16410"     "16412"    
 [331] "16433"     "16450"     "16477"     "16532"     "16542"     "16590"    
 [337] "16601"     "16650"     "16669"     "16691"     "16777"     "16783"    
 [343] "16833"     "16842"     "16846"     "16847"     "16848"     "16859"    
 [349] "16866"     "16867"     "16869"     "16871"     "16872"     "16875"    
 [355] "16876"     "16878"     "16886"     "16952"     "16970"     "16974"    
 [361] "17125"     "17128"     "17129"     "17149"     "17171"     "17173"    
 [367] "17191"     "17221"     "17235"     "17240"     "17242"     "17256"    
 [373] "17283"     "17289"     "17295"     "17300"     "17304"     "17311"    
 [379] "17319"     "17345"     "17350"     "17381"     "17390"     "17395"    
 [385] "17427"     "17450"     "17451"     "17535"     "17684"     "17685"    
 [391] "17686"     "17687"     "17688"     "17701"     "17702"     "17761"    
 [397] "17771"     "17776"     "17836"     "17864"     "17886"     "17977"    
 [403] "17978"     "17979"     "17986"     "18000"     "18004"     "18005"    
 [409] "18011"     "18014"     "18022"     "18072"     "18095"     "18119"    
 [415] "18121"     "18127"     "18128"     "18129"     "18142"     "18159"    
 [421] "18168"     "18194"     "18211"     "18285"     "18286"     "18291"    
 [427] "18292"     "18387"     "18413"     "18417"     "18426"     "18429"    
 [433] "18430"     "18431"     "18436"     "18441"     "18442"     "18472"    
 [439] "18475"     "18476"     "18504"     "18507"     "18514"     "18551"    
 [445] "18552"     "18555"     "18591"     "18595"     "18606"     "18617"    
 [451] "18663"     "18667"     "18671"     "18747"     "18749"     "18763"    
 [457] "18764"     "18766"     "18775"     "18776"     "18783"     "18787"    
 [463] "18791"     "18792"     "18793"     "18795"     "18799"     "18802"    
 [469] "18811"     "18812"     "18814"     "18815"     "18817"     "18830"    
 [475] "18858"     "18861"     "18952"     "19014"     "19015"     "19016"    
 [481] "19049"     "19052"     "19059"     "19090"     "19109"     "19110"    
 [487] "19111"     "19112"     "19113"     "19114"     "19116"     "19118"    
 [493] "19119"     "19120"     "19143"     "19156"     "19183"     "19204"    
 [499] "19211"     "19214"     "19215"     "19219"     "19223"     "19225"    
 [505] "19229"     "19242"     "19247"     "19275"     "19288"     "19294"    
 [511] "19317"     "19339"     "19353"     "19355"     "19357"     "19359"    
 [517] "19360"     "19361"     "19362"     "19364"     "19366"     "19401"    
 [523] "19411"     "19662"     "19664"     "19701"     "19725"     "19733"    
 [529] "19735"     "19773"     "19821"     "19886"     "20017"     "20104"    
 [535] "20112"     "20181"     "20182"     "20315"     "20317"     "20319"    
 [541] "20322"     "20346"     "20363"     "20377"     "20397"     "20415"    
 [547] "20423"     "20437"     "20473"     "20474"     "20475"     "20520"    
 [553] "20541"     "20613"     "20655"     "20662"     "20670"     "20671"    
 [559] "20674"     "20675"     "20681"     "20682"     "20683"     "20686"    
 [565] "20687"     "20690"     "20708"     "20719"     "20720"     "20724"    
 [571] "20729"     "20730"     "20732"     "20733"     "20744"     "20758"    
 [577] "20779"     "20826"     "20843"     "20848"     "20850"     "20851"    
 [583] "20860"     "20869"     "20871"     "20873"     "20878"     "20892"    
 [589] "20897"     "20899"     "20905"     "20910"     "20957"     "20962"    
 [595] "20997"     "21333"     "21334"     "21336"     "21337"     "21338"    
 [601] "21357"     "21386"     "21405"     "21410"     "21412"     "21414"    
 [607] "21416"     "21425"     "21454"     "21463"     "21645"     "21674"    
 [613] "21679"     "21744"     "21749"     "21803"     "21808"     "21812"    
 [619] "21821"     "21823"     "21824"     "21830"     "21833"     "21834"    
 [625] "21843"     "21849"     "21857"     "21869"     "21887"     "21923"    
 [631] "21945"     "21958"     "21959"     "21973"     "21974"     "22022"    
 [637] "22026"     "22061"     "22064"     "22065"     "22068"     "22092"    
 [643] "22113"     "22114"     "22115"     "22127"     "22137"     "22174"    
 [649] "22187"     "22209"     "22210"     "22215"     "22249"     "22329"    
 [655] "22334"     "22337"     "22339"     "22353"     "22371"     "22384"    
 [661] "22412"     "22413"     "22415"     "22417"     "22418"     "22421"    
 [667] "22422"     "22431"     "22441"     "22445"     "22446"     "22589"    
 [673] "22632"     "22635"     "22661"     "22668"     "22691"     "22694"    
 [679] "22696"     "22697"     "22698"     "22701"     "22702"     "22715"    
 [685] "22762"     "22764"     "22768"     "22786"     "22787"     "22788"    
 [691] "22789"     "23793"     "23885"     "23887"     "23920"     "23950"    
 [697] "23967"     "23968"     "23980"     "23991"     "23997"     "24061"    
 [703] "24084"     "24086"     "24127"     "24128"     "26357"     "26362"    
 [709] "26366"     "26370"     "26380"     "26384"     "26395"     "26407"    
 [715] "26413"     "26416"     "26417"     "26423"     "26434"     "26437"    
 [721] "26564"     "26565"     "26900"     "26909"     "26910"     "26920"    
 [727] "26927"     "26934"     "26942"     "26946"     "26972"     "27061"    
 [733] "27083"     "27084"     "27206"     "27222"     "27354"     "27356"    
 [739] "27372"     "27386"     "28036"     "28078"     "28088"     "28105"    
 [745] "28114"     "28135"     "29871"     "29876"     "30054"     "30841"    
 [751] "30939"     "30953"     "30959"     "50500"     "50501"     "50505"    
 [757] "50525"     "50722"     "50785"     "50790"     "50796"     "50878"    
 [763] "50915"     "51789"     "51792"     "51885"     "51938"     "52020"    
 [769] "52028"     "52679"     "52683"     "52864"     "53381"     "53419"    
 [775] "53422"     "53424"     "53601"     "53604"     "53614"     "53814"    
 [781] "53878"     "53885"     "53897"     "53975"     "54003"     "54004"    
 [787] "54137"     "54140"     "54204"     "54383"     "54388"     "54418"    
 [793] "54427"     "54486"     "54524"     "54562"     "54608"     "54611"    
 [799] "54650"     "54725"     "55925"     "55978"     "55993"     "55994"    
 [805] "56092"     "56094"     "56096"     "56213"     "56218"     "56220"    
 [811] "56223"     "56228"     "56274"     "56291"     "56296"     "56312"    
 [817] "56334"     "56335"     "56371"     "56406"     "56436"     "56449"    
 [823] "56484"     "56503"     "56523"     "56526"     "56622"     "56635"    
 [829] "56693"     "56710"     "56711"     "56717"     "56739"     "56746"    
 [835] "57256"     "57264"     "57320"     "57746"     "57749"     "57815"    
 [841] "57816"     "57908"     "58186"     "58226"     "58230"     "58231"    
 [847] "58864"     "58991"     "58998"     "59030"     "59083"     "60530"    
 [853] "60534"     "60597"     "63872"     "64009"     "64335"     "64383"    
 [859] "64707"     "64931"     "65247"     "65971"     "66193"     "66197"    
 [865] "66313"     "66392"     "66404"     "66515"     "66573"     "66634"    
 [871] "66654"     "66707"     "66712"     "66713"     "66720"     "66722"    
 [877] "66793"     "66923"     "66977"     "66983"     "67000"     "67010"    
 [883] "67030"     "67042"     "67052"     "67077"     "67121"     "67141"    
 [889] "67181"     "67204"     "67231"     "67310"     "67331"     "67333"    
 [895] "67345"     "67374"     "67378"     "67402"     "67504"     "67505"    
 [901] "67537"     "67555"     "67561"     "67652"     "67690"     "67713"    
 [907] "67753"     "67869"     "67909"     "67946"     "67968"     "67971"    
 [913] "67981"     "68107"     "68166"     "68170"     "68231"     "68265"    
 [919] "68275"     "68298"     "68328"     "68549"     "68708"     "68767"    
 [925] "68911"     "68922"     "68981"     "69032"     "69064"     "69260"    
 [931] "69286"     "69287"     "69306"     "69307"     "69310"     "69329"    
 [937] "69376"     "69444"     "69538"     "69546"     "69707"     "69716"    
 [943] "69852"     "69865"     "69928"     "69982"     "70069"     "70093"    
 [949] "70099"     "70231"     "70235"     "70248"     "70375"     "70441"    
 [955] "70465"     "70503"     "70691"     "70772"     "70840"     "70862"    
 [961] "70873"     "70891"     "70918"     "70956"     "70977"     "71037"    
 [967] "71062"     "71089"     "71099"     "71132"     "71175"     "71233"    
 [973] "71241"     "71242"     "71371"     "71567"     "71709"     "71711"    
 [979] "71765"     "71830"     "71836"     "71840"     "71841"     "71846"    
 [985] "71904"     "71914"     "71950"     "71981"     "72135"     "72148"    
 [991] "72162"     "72236"     "72415"     "72469"     "72504"     "72508"    
 [997] "72568"     "72634"     "72780"     "72787"     "72891"     "72938"    
[1003] "73242"     "73244"     "73296"     "73316"     "73329"     "73336"    
[1009] "73412"     "73456"     "73472"     "73542"     "73616"     "73673"    
[1015] "73677"     "73679"     "73721"     "74041"     "74052"     "74068"    
[1021] "74075"     "74090"     "74117"     "74174"     "74188"     "74229"    
[1027] "74237"     "74267"     "74286"     "74288"     "74297"     "74309"    
[1033] "74354"     "74360"     "74369"     "74377"     "74386"     "74401"    
[1039] "74434"     "74446"     "74450"     "74468"     "74469"     "74666"    
[1045] "74691"     "74708"     "74711"     "74716"     "74754"     "74847"    
[1051] "74927"     "75002"     "75019"     "75033"     "75140"     "75178"    
[1057] "75202"     "75388"     "75410"     "75437"     "75459"     "75469"    
[1063] "75514"     "75533"     "75571"     "75596"     "75605"     "75622"    
[1069] "75642"     "75646"     "75753"     "75801"     "75826"     "75828"    
[1075] "75909"     "76378"     "76407"     "76421"     "76457"     "76486"    
[1081] "76499"     "76573"     "76606"     "76718"     "76800"     "76850"    
[1087] "76856"     "76858"     "76867"     "76915"     "76925"     "76943"    
[1093] "77053"     "77128"     "77424"     "77595"     "77609"     "77963"    
[1099] "77980"     "78081"     "78118"     "78124"     "78284"     "78619"    
[1105] "78634"     "78658"     "78784"     "78801"     "78803"     "78925"    
[1111] "80297"     "80517"     "80838"     "80884"     "80912"     "81018"    
[1117] "83434"     "83456"     "83557"     "83558"     "83560"     "83561"    
[1123] "83964"     "83984"     "93684"     "93736"     "93757"     "93759"    
[1129] "93760"     "93837"     "93960"     "94109"     "94221"     "94224"    
[1135] "94244"     "94246"     "97086"     "97165"     "98558"     "98711"    
[1141] "99412"     "99929"     "100121"    "100155"    "100317"    "100535"   
[1147] "100986"    "101187"    "101476"    "102774"    "102991"    "103468"   
[1153] "103554"    "103583"    "103733"    "103768"    "104083"    "104111"   
[1159] "104148"    "104156"    "104263"    "104271"    "104310"    "104346"   
[1165] "104362"    "104601"    "104799"    "104806"    "105349"    "105511"   
[1171] "105988"    "106389"    "106757"    "107515"    "107586"    "107626"   
[1177] "107656"    "107849"    "107970"    "107995"    "108829"    "108961"   
[1183] "109685"    "109689"    "109727"    "109785"    "110012"    "110082"   
[1189] "110084"    "110147"    "110355"    "110459"    "110542"    "110957"   
[1195] "110958"    "112405"    "114602"    "114606"    "114642"    "114661"   
[1201] "114662"    "114714"    "114875"    "116837"    "140498"    "140557"   
[1207] "170676"    "171285"    "171429"    "171506"    "192119"    "192176"   
[1213] "192195"    "192199"    "192236"    "192897"    "193322"    "193838"   
[1219] "194908"    "195434"    "207165"    "207182"    "207304"    "207352"   
[1225] "207607"    "207686"    "208144"    "208169"    "208188"    "208727"   
[1231] "209011"    "209091"    "209351"    "210510"    "210529"    "210554"   
[1237] "211064"    "211484"    "211651"    "212517"    "212670"    "212937"   
[1243] "213081"    "213236"    "213272"    "213389"    "213402"    "213541"   
[1249] "213742"    "214105"    "214253"    "214290"    "214292"    "214321"   
[1255] "214384"    "214572"    "214575"    "214593"    "214901"    "215028"   
[1261] "215029"    "215095"    "215387"    "215854"    "216350"    "216725"   
[1267] "216869"    "217039"    "217116"    "217216"    "217325"    "217341"   
[1273] "217715"    "217716"    "218214"    "218454"    "219038"    "223593"   
[1279] "223697"    "223825"    "223921"    "223989"    "224045"    "224171"   
[1285] "224661"    "224727"    "224826"    "224902"    "225182"    "225497"   
[1291] "225865"    "226049"    "226090"    "226162"    "226265"    "226841"   
[1297] "227210"    "227394"    "227615"    "227631"    "227736"    "228421"   
[1303] "228980"    "229227"    "229357"    "229700"    "229841"    "230103"   
[1309] "230126"    "230594"    "230809"    "230861"    "230899"    "231051"   
[1315] "231386"    "231600"    "231633"    "231672"    "231832"    "231912"   
[1321] "232174"    "232223"    "232286"    "232345"    "232664"    "232816"   
[1327] "233276"    "234857"    "235072"    "235320"    "235330"    "235345"   
[1333] "235380"    "235559"    "235626"    "235628"    "235682"    "236266"   
[1339] "236899"    "237336"    "237625"    "237911"    "238055"    "238057"   
[1345] "238247"    "238328"    "238330"    "238405"    "238406"    "239083"   
[1351] "239167"    "239528"    "239731"    "240069"    "240255"    "240590"   
[1357] "240697"    "240725"    "240899"    "241116"    "241516"    "241624"   
[1363] "242202"    "242523"    "242620"    "243862"    "243866"    "243897"   
[1369] "243905"    "244486"    "244495"    "244551"    "245000"    "245865"   
[1375] "246747"    "252828"    "252866"    "252868"    "252967"    "252973"   
[1381] "259279"    "260305"    "263876"    "264134"    "268396"    "268420"   
[1387] "268465"    "268491"    "268591"    "268697"    "268755"    "268860"   
[1393] "268903"    "268930"    "269254"    "269275"    "269610"    "269682"   
[1399] "269701"    "270624"    "271036"    "271127"    "271564"    "271639"   
[1405] "272643"    "276920"    "278240"    "280287"    "280667"    "280668"   
[1411] "317653"    "319177"    "319448"    "319953"    "320022"    "320244"   
[1417] "320277"    "320558"    "320752"    "320790"    "327826"    "328019"   
[1423] "328365"    "328401"    "328440"    "328580"    "328845"    "329557"   
[1429] "329954"    "330149"    "330188"    "330319"    "330409"    "330470"   
[1435] "330830"    "330890"    "331046"    "331416"    "332110"    "332397"   
[1441] "353188"    "378430"    "378462"    "380654"    "380684"    "380702"   
[1447] "380709"    "380773"    "380855"    "380993"    "380994"    "381022"   
[1453] "381157"    "381196"    "381290"    "381404"    "381489"    "381677"   
[1459] "381678"    "381759"    "382007"    "382077"    "382217"    "382275"   
[1465] "382277"    "382301"    "383491"    "384619"    "384806"    "384813"   
[1471] "387139"    "387140"    "387153"    "387156"    "387161"    "387162"   
[1477] "387177"    "387178"    "387179"    "387188"    "387198"    "387218"   
[1483] "387244"    "387245"    "387246"    "387247"    "399599"    "433700"   
[1489] "434438"    "434768"    "434784"    "434794"    "442829"    "544736"   
[1495] "545156"    "546055"    "546118"    "546272"    "546282"    "574428"   
[1501] "574437"    "574438"    "619517"    "619697"    "619991"    "622480"   
[1507] "622554"    "623474"    "625249"    "625662"    "627081"    "628438"   
[1513] "637277"    "664799"    "664829"    "665270"    "665780"    "666317"   
[1519] "666528"    "668110"    "668929"    "671232"    "671564"    "723849"   
[1525] "723868"    "723886"    "723932"    "723939"    "723955"    "723956"   
[1531] "723962"    "723965"    "723966"    "735262"    "735309"    "751535"   
[1537] "100009600" "100038417" "100038489" "100038977" "100039030" "100039065"
[1543] "100039120" "100039842" "100039905" "100040608" "100040894" "100042109"
[1549] "100042175" "100042922" "100042929" "100042931" "100042939" "100042943"
[1555] "100042944" "100042946" "100043216" "100048534" "100049545" "100049546"
[1561] "100049548" "100113365" "100124460" "100124479" "100124480" "100190765"
[1567] "100270744" "100503361" "100504642" "100861637" "100861881" "101055773"
[1573] "101056116" "101056210" "102443351" "102631559" "102633564" "102636501"
[1579] "102638101" "102638793" "102639094" "102639490" "102639895" "105247282"
[1585] "108168511" "108168530" "108168552" "108168557" "108168582" "108168594"
[1591] "113523646"

$`GO:0000012`
 [1] "11545"  "14211"  "22064"  "22594"  "66408"  "70099"  "71991"  "72103" 
 [9] "93759"  "104884" "319583" "319955"

> # 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:0002282                5                 5        1.6379883  0.0001089845
GO:0019886               16                16        1.0776253  0.0002145139
GO:1905146               17                17        1.0606304  0.0002244091
GO:1900424               17                15        1.0721442  0.0003038984
GO:1900426               12                10        1.1666016  0.0004664378
GO:0002495               21                21        0.9671930  0.0004860756
GO:0002478               27                26        0.9072525  0.0005366052
GO:0007039               19                19        0.9829004  0.0005518269
GO:0002504               22                22        0.9409343  0.0006380768
GO:0140059               10                 9        1.1540213  0.0008533323
                                                                                  geneSetDescription
GO:0002282                                    microglial cell activation involved in immune response
GO:0019886         antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:1905146                                                       lysosomal protein catabolic process
GO:1900424                                               regulation of defense response to bacterium
GO:1900426                                      positive regulation of defense response to bacterium
GO:0002495                   antigen processing and presentation of peptide antigen via MHC class II
GO:0002478                          antigen processing and presentation of exogenous peptide antigen
GO:0007039                                                  protein catabolic process in the vacuole
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
GO:0140059                                                                     dendrite arborization
> # output changes with annotation version !
> 
> plotGOgraph(object = mlpObject, main = "test of main")
Loading required namespace: Rgraphviz
Loading required namespace: GOstats
Loading required namespace: gplots
> 
> 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 
  48.03    3.78   52.00 

MLP.Rcheck/tests_x64/test.MLP.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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
> 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)
> library(org.Mm.eg.db) # for mouse
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 object is masked from 'package:limma':

    plotMA

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

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 objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows


> 
> 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 namespace: GO.db

   user  system elapsed 
  24.18    1.11   25.28 
> goGeneSet[1:3]
$`GO:0000002`
 [1] "11545"  "12628"  "16882"  "17258"  "17527"  "19017"  "21975"  "22059" 
 [9] "23797"  "27393"  "27395"  "27397"  "50776"  "57813"  "70556"  "72170" 
[17] "72962"  "74143"  "74528"  "83408"  "192287" "216021" "216805" "230784"
[25] "327762" "408022"

$`GO:0000003`
   [1] "11287"     "11352"     "11421"     "11430"     "11434"     "11441"    
   [7] "11477"     "11479"     "11480"     "11486"     "11495"     "11497"    
  [13] "11498"     "11499"     "11504"     "11516"     "11517"     "11535"    
  [19] "11551"     "11552"     "11553"     "11576"     "11600"     "11606"    
  [25] "11614"     "11622"     "11625"     "11643"     "11647"     "11651"    
  [31] "11674"     "11705"     "11747"     "11757"     "11774"     "11789"    
  [37] "11797"     "11804"     "11819"     "11820"     "11835"     "11839"    
  [43] "11857"     "11863"     "11865"     "11883"     "11920"     "11998"    
  [49] "12009"     "12018"     "12028"     "12034"     "12041"     "12043"    
  [55] "12048"     "12050"     "12053"     "12124"     "12125"     "12142"    
  [61] "12155"     "12159"     "12160"     "12161"     "12162"     "12163"    
  [67] "12164"     "12166"     "12167"     "12168"     "12173"     "12190"    
  [73] "12192"     "12211"     "12215"     "12235"     "12236"     "12237"    
  [79] "12261"     "12266"     "12290"     "12305"     "12310"     "12316"    
  [85] "12317"     "12323"     "12344"     "12363"     "12366"     "12380"    
  [91] "12387"     "12394"     "12411"     "12416"     "12426"     "12427"    
  [97] "12442"     "12443"     "12447"     "12448"     "12449"     "12458"    
 [103] "12461"     "12462"     "12464"     "12465"     "12466"     "12468"    
 [109] "12469"     "12505"     "12527"     "12530"     "12531"     "12532"    
 [115] "12550"     "12566"     "12576"     "12577"     "12589"     "12591"    
 [121] "12592"     "12593"     "12606"     "12608"     "12617"     "12638"    
 [127] "12640"     "12659"     "12702"     "12704"     "12705"     "12745"    
 [133] "12753"     "12767"     "12801"     "12804"     "12841"     "12846"    
 [139] "12877"     "12916"     "12918"     "12919"     "12929"     "12946"    
 [145] "12977"     "12981"     "13006"     "13030"     "13039"     "13046"    
 [151] "13052"     "13070"     "13075"     "13123"     "13134"     "13164"    
 [157] "13166"     "13205"     "13206"     "13363"     "13382"     "13383"    
 [163] "13393"     "13404"     "13411"     "13435"     "13487"     "13488"    
 [169] "13491"     "13492"     "13498"     "13524"     "13525"     "13526"    
 [175] "13529"     "13615"     "13617"     "13618"     "13649"     "13653"    
 [181] "13667"     "13731"     "13813"     "13819"     "13852"     "13854"    
 [187] "13856"     "13857"     "13866"     "13870"     "13874"     "13875"    
 [193] "13982"     "13983"     "13984"     "14008"     "14011"     "14087"    
 [199] "14088"     "14155"     "14160"     "14165"     "14178"     "14179"    
 [205] "14180"     "14183"     "14211"     "14228"     "14238"     "14275"    
 [211] "14276"     "14283"     "14308"     "14309"     "14313"     "14347"    
 [217] "14366"     "14367"     "14388"     "14402"     "14421"     "14431"    
 [223] "14447"     "14453"     "14460"     "14461"     "14462"     "14463"    
 [229] "14531"     "14536"     "14566"     "14595"     "14598"     "14609"    
 [235] "14610"     "14620"     "14622"     "14632"     "14633"     "14654"    
 [241] "14658"     "14682"     "14705"     "14714"     "14725"     "14748"    
 [247] "14764"     "14766"     "14782"     "14784"     "14810"     "14815"    
 [253] "14824"     "15013"     "15018"     "15078"     "15081"     "15110"    
 [259] "15170"     "15182"     "15194"     "15204"     "15205"     "15209"    
 [265] "15211"     "15212"     "15213"     "15214"     "15221"     "15235"    
 [271] "15247"     "15251"     "15270"     "15361"     "15364"     "15373"    
 [277] "15375"     "15377"     "15378"     "15387"     "15395"     "15396"    
 [283] "15398"     "15405"     "15408"     "15423"     "15430"     "15431"    
 [289] "15433"     "15438"     "15446"     "15463"     "15482"     "15484"    
 [295] "15486"     "15487"     "15488"     "15499"     "15500"     "15502"    
 [301] "15511"     "15512"     "15516"     "15567"     "15570"     "15574"    
 [307] "15894"     "15904"     "16000"     "16001"     "16002"     "16007"    
 [313] "16011"     "16147"     "16153"     "16157"     "16173"     "16175"    
 [319] "16176"     "16319"     "16322"     "16323"     "16324"     "16330"    
 [325] "16336"     "16337"     "16365"     "16401"     "16410"     "16412"    
 [331] "16433"     "16450"     "16477"     "16532"     "16542"     "16590"    
 [337] "16601"     "16650"     "16669"     "16691"     "16777"     "16783"    
 [343] "16833"     "16842"     "16846"     "16847"     "16848"     "16859"    
 [349] "16866"     "16867"     "16869"     "16871"     "16872"     "16875"    
 [355] "16876"     "16878"     "16886"     "16952"     "16970"     "16974"    
 [361] "17125"     "17128"     "17129"     "17149"     "17171"     "17173"    
 [367] "17191"     "17221"     "17235"     "17240"     "17242"     "17256"    
 [373] "17283"     "17289"     "17295"     "17300"     "17304"     "17311"    
 [379] "17319"     "17345"     "17350"     "17381"     "17390"     "17395"    
 [385] "17427"     "17450"     "17451"     "17535"     "17684"     "17685"    
 [391] "17686"     "17687"     "17688"     "17701"     "17702"     "17761"    
 [397] "17771"     "17776"     "17836"     "17864"     "17886"     "17977"    
 [403] "17978"     "17979"     "17986"     "18000"     "18004"     "18005"    
 [409] "18011"     "18014"     "18022"     "18072"     "18095"     "18119"    
 [415] "18121"     "18127"     "18128"     "18129"     "18142"     "18159"    
 [421] "18168"     "18194"     "18211"     "18285"     "18286"     "18291"    
 [427] "18292"     "18387"     "18413"     "18417"     "18426"     "18429"    
 [433] "18430"     "18431"     "18436"     "18441"     "18442"     "18472"    
 [439] "18475"     "18476"     "18504"     "18507"     "18514"     "18551"    
 [445] "18552"     "18555"     "18591"     "18595"     "18606"     "18617"    
 [451] "18663"     "18667"     "18671"     "18747"     "18749"     "18763"    
 [457] "18764"     "18766"     "18775"     "18776"     "18783"     "18787"    
 [463] "18791"     "18792"     "18793"     "18795"     "18799"     "18802"    
 [469] "18811"     "18812"     "18814"     "18815"     "18817"     "18830"    
 [475] "18858"     "18861"     "18952"     "19014"     "19015"     "19016"    
 [481] "19049"     "19052"     "19059"     "19090"     "19109"     "19110"    
 [487] "19111"     "19112"     "19113"     "19114"     "19116"     "19118"    
 [493] "19119"     "19120"     "19143"     "19156"     "19183"     "19204"    
 [499] "19211"     "19214"     "19215"     "19219"     "19223"     "19225"    
 [505] "19229"     "19242"     "19247"     "19275"     "19288"     "19294"    
 [511] "19317"     "19339"     "19353"     "19355"     "19357"     "19359"    
 [517] "19360"     "19361"     "19362"     "19364"     "19366"     "19401"    
 [523] "19411"     "19662"     "19664"     "19701"     "19725"     "19733"    
 [529] "19735"     "19773"     "19821"     "19886"     "20017"     "20104"    
 [535] "20112"     "20181"     "20182"     "20315"     "20317"     "20319"    
 [541] "20322"     "20346"     "20363"     "20377"     "20397"     "20415"    
 [547] "20423"     "20437"     "20473"     "20474"     "20475"     "20520"    
 [553] "20541"     "20613"     "20655"     "20662"     "20670"     "20671"    
 [559] "20674"     "20675"     "20681"     "20682"     "20683"     "20686"    
 [565] "20687"     "20690"     "20708"     "20719"     "20720"     "20724"    
 [571] "20729"     "20730"     "20732"     "20733"     "20744"     "20758"    
 [577] "20779"     "20826"     "20843"     "20848"     "20850"     "20851"    
 [583] "20860"     "20869"     "20871"     "20873"     "20878"     "20892"    
 [589] "20897"     "20899"     "20905"     "20910"     "20957"     "20962"    
 [595] "20997"     "21333"     "21334"     "21336"     "21337"     "21338"    
 [601] "21357"     "21386"     "21405"     "21410"     "21412"     "21414"    
 [607] "21416"     "21425"     "21454"     "21463"     "21645"     "21674"    
 [613] "21679"     "21744"     "21749"     "21803"     "21808"     "21812"    
 [619] "21821"     "21823"     "21824"     "21830"     "21833"     "21834"    
 [625] "21843"     "21849"     "21857"     "21869"     "21887"     "21923"    
 [631] "21945"     "21958"     "21959"     "21973"     "21974"     "22022"    
 [637] "22026"     "22061"     "22064"     "22065"     "22068"     "22092"    
 [643] "22113"     "22114"     "22115"     "22127"     "22137"     "22174"    
 [649] "22187"     "22209"     "22210"     "22215"     "22249"     "22329"    
 [655] "22334"     "22337"     "22339"     "22353"     "22371"     "22384"    
 [661] "22412"     "22413"     "22415"     "22417"     "22418"     "22421"    
 [667] "22422"     "22431"     "22441"     "22445"     "22446"     "22589"    
 [673] "22632"     "22635"     "22661"     "22668"     "22691"     "22694"    
 [679] "22696"     "22697"     "22698"     "22701"     "22702"     "22715"    
 [685] "22762"     "22764"     "22768"     "22786"     "22787"     "22788"    
 [691] "22789"     "23793"     "23885"     "23887"     "23920"     "23950"    
 [697] "23967"     "23968"     "23980"     "23991"     "23997"     "24061"    
 [703] "24084"     "24086"     "24127"     "24128"     "26357"     "26362"    
 [709] "26366"     "26370"     "26380"     "26384"     "26395"     "26407"    
 [715] "26413"     "26416"     "26417"     "26423"     "26434"     "26437"    
 [721] "26564"     "26565"     "26900"     "26909"     "26910"     "26920"    
 [727] "26927"     "26934"     "26942"     "26946"     "26972"     "27061"    
 [733] "27083"     "27084"     "27206"     "27222"     "27354"     "27356"    
 [739] "27372"     "27386"     "28036"     "28078"     "28088"     "28105"    
 [745] "28114"     "28135"     "29871"     "29876"     "30054"     "30841"    
 [751] "30939"     "30953"     "30959"     "50500"     "50501"     "50505"    
 [757] "50525"     "50722"     "50785"     "50790"     "50796"     "50878"    
 [763] "50915"     "51789"     "51792"     "51885"     "51938"     "52020"    
 [769] "52028"     "52679"     "52683"     "52864"     "53381"     "53419"    
 [775] "53422"     "53424"     "53601"     "53604"     "53614"     "53814"    
 [781] "53878"     "53885"     "53897"     "53975"     "54003"     "54004"    
 [787] "54137"     "54140"     "54204"     "54383"     "54388"     "54418"    
 [793] "54427"     "54486"     "54524"     "54562"     "54608"     "54611"    
 [799] "54650"     "54725"     "55925"     "55978"     "55993"     "55994"    
 [805] "56092"     "56094"     "56096"     "56213"     "56218"     "56220"    
 [811] "56223"     "56228"     "56274"     "56291"     "56296"     "56312"    
 [817] "56334"     "56335"     "56371"     "56406"     "56436"     "56449"    
 [823] "56484"     "56503"     "56523"     "56526"     "56622"     "56635"    
 [829] "56693"     "56710"     "56711"     "56717"     "56739"     "56746"    
 [835] "57256"     "57264"     "57320"     "57746"     "57749"     "57815"    
 [841] "57816"     "57908"     "58186"     "58226"     "58230"     "58231"    
 [847] "58864"     "58991"     "58998"     "59030"     "59083"     "60530"    
 [853] "60534"     "60597"     "63872"     "64009"     "64335"     "64383"    
 [859] "64707"     "64931"     "65247"     "65971"     "66193"     "66197"    
 [865] "66313"     "66392"     "66404"     "66515"     "66573"     "66634"    
 [871] "66654"     "66707"     "66712"     "66713"     "66720"     "66722"    
 [877] "66793"     "66923"     "66977"     "66983"     "67000"     "67010"    
 [883] "67030"     "67042"     "67052"     "67077"     "67121"     "67141"    
 [889] "67181"     "67204"     "67231"     "67310"     "67331"     "67333"    
 [895] "67345"     "67374"     "67378"     "67402"     "67504"     "67505"    
 [901] "67537"     "67555"     "67561"     "67652"     "67690"     "67713"    
 [907] "67753"     "67869"     "67909"     "67946"     "67968"     "67971"    
 [913] "67981"     "68107"     "68166"     "68170"     "68231"     "68265"    
 [919] "68275"     "68298"     "68328"     "68549"     "68708"     "68767"    
 [925] "68911"     "68922"     "68981"     "69032"     "69064"     "69260"    
 [931] "69286"     "69287"     "69306"     "69307"     "69310"     "69329"    
 [937] "69376"     "69444"     "69538"     "69546"     "69707"     "69716"    
 [943] "69852"     "69865"     "69928"     "69982"     "70069"     "70093"    
 [949] "70099"     "70231"     "70235"     "70248"     "70375"     "70441"    
 [955] "70465"     "70503"     "70691"     "70772"     "70840"     "70862"    
 [961] "70873"     "70891"     "70918"     "70956"     "70977"     "71037"    
 [967] "71062"     "71089"     "71099"     "71132"     "71175"     "71233"    
 [973] "71241"     "71242"     "71371"     "71567"     "71709"     "71711"    
 [979] "71765"     "71830"     "71836"     "71840"     "71841"     "71846"    
 [985] "71904"     "71914"     "71950"     "71981"     "72135"     "72148"    
 [991] "72162"     "72236"     "72415"     "72469"     "72504"     "72508"    
 [997] "72568"     "72634"     "72780"     "72787"     "72891"     "72938"    
[1003] "73242"     "73244"     "73296"     "73316"     "73329"     "73336"    
[1009] "73412"     "73456"     "73472"     "73542"     "73616"     "73673"    
[1015] "73677"     "73679"     "73721"     "74041"     "74052"     "74068"    
[1021] "74075"     "74090"     "74117"     "74174"     "74188"     "74229"    
[1027] "74237"     "74267"     "74286"     "74288"     "74297"     "74309"    
[1033] "74354"     "74360"     "74369"     "74377"     "74386"     "74401"    
[1039] "74434"     "74446"     "74450"     "74468"     "74469"     "74666"    
[1045] "74691"     "74708"     "74711"     "74716"     "74754"     "74847"    
[1051] "74927"     "75002"     "75019"     "75033"     "75140"     "75178"    
[1057] "75202"     "75388"     "75410"     "75437"     "75459"     "75469"    
[1063] "75514"     "75533"     "75571"     "75596"     "75605"     "75622"    
[1069] "75642"     "75646"     "75753"     "75801"     "75826"     "75828"    
[1075] "75909"     "76378"     "76407"     "76421"     "76457"     "76486"    
[1081] "76499"     "76573"     "76606"     "76718"     "76800"     "76850"    
[1087] "76856"     "76858"     "76867"     "76915"     "76925"     "76943"    
[1093] "77053"     "77128"     "77424"     "77595"     "77609"     "77963"    
[1099] "77980"     "78081"     "78118"     "78124"     "78284"     "78619"    
[1105] "78634"     "78658"     "78784"     "78801"     "78803"     "78925"    
[1111] "80297"     "80517"     "80838"     "80884"     "80912"     "81018"    
[1117] "83434"     "83456"     "83557"     "83558"     "83560"     "83561"    
[1123] "83964"     "83984"     "93684"     "93736"     "93757"     "93759"    
[1129] "93760"     "93837"     "93960"     "94109"     "94221"     "94224"    
[1135] "94244"     "94246"     "97086"     "97165"     "98558"     "98711"    
[1141] "99412"     "99929"     "100121"    "100155"    "100317"    "100535"   
[1147] "100986"    "101187"    "101476"    "102774"    "102991"    "103468"   
[1153] "103554"    "103583"    "103733"    "103768"    "104083"    "104111"   
[1159] "104148"    "104156"    "104263"    "104271"    "104310"    "104346"   
[1165] "104362"    "104601"    "104799"    "104806"    "105349"    "105511"   
[1171] "105988"    "106389"    "106757"    "107515"    "107586"    "107626"   
[1177] "107656"    "107849"    "107970"    "107995"    "108829"    "108961"   
[1183] "109685"    "109689"    "109727"    "109785"    "110012"    "110082"   
[1189] "110084"    "110147"    "110355"    "110459"    "110542"    "110957"   
[1195] "110958"    "112405"    "114602"    "114606"    "114642"    "114661"   
[1201] "114662"    "114714"    "114875"    "116837"    "140498"    "140557"   
[1207] "170676"    "171285"    "171429"    "171506"    "192119"    "192176"   
[1213] "192195"    "192199"    "192236"    "192897"    "193322"    "193838"   
[1219] "194908"    "195434"    "207165"    "207182"    "207304"    "207352"   
[1225] "207607"    "207686"    "208144"    "208169"    "208188"    "208727"   
[1231] "209011"    "209091"    "209351"    "210510"    "210529"    "210554"   
[1237] "211064"    "211484"    "211651"    "212517"    "212670"    "212937"   
[1243] "213081"    "213236"    "213272"    "213389"    "213402"    "213541"   
[1249] "213742"    "214105"    "214253"    "214290"    "214292"    "214321"   
[1255] "214384"    "214572"    "214575"    "214593"    "214901"    "215028"   
[1261] "215029"    "215095"    "215387"    "215854"    "216350"    "216725"   
[1267] "216869"    "217039"    "217116"    "217216"    "217325"    "217341"   
[1273] "217715"    "217716"    "218214"    "218454"    "219038"    "223593"   
[1279] "223697"    "223825"    "223921"    "223989"    "224045"    "224171"   
[1285] "224661"    "224727"    "224826"    "224902"    "225182"    "225497"   
[1291] "225865"    "226049"    "226090"    "226162"    "226265"    "226841"   
[1297] "227210"    "227394"    "227615"    "227631"    "227736"    "228421"   
[1303] "228980"    "229227"    "229357"    "229700"    "229841"    "230103"   
[1309] "230126"    "230594"    "230809"    "230861"    "230899"    "231051"   
[1315] "231386"    "231600"    "231633"    "231672"    "231832"    "231912"   
[1321] "232174"    "232223"    "232286"    "232345"    "232664"    "232816"   
[1327] "233276"    "234857"    "235072"    "235320"    "235330"    "235345"   
[1333] "235380"    "235559"    "235626"    "235628"    "235682"    "236266"   
[1339] "236899"    "237336"    "237625"    "237911"    "238055"    "238057"   
[1345] "238247"    "238328"    "238330"    "238405"    "238406"    "239083"   
[1351] "239167"    "239528"    "239731"    "240069"    "240255"    "240590"   
[1357] "240697"    "240725"    "240899"    "241116"    "241516"    "241624"   
[1363] "242202"    "242523"    "242620"    "243862"    "243866"    "243897"   
[1369] "243905"    "244486"    "244495"    "244551"    "245000"    "245865"   
[1375] "246747"    "252828"    "252866"    "252868"    "252967"    "252973"   
[1381] "259279"    "260305"    "263876"    "264134"    "268396"    "268420"   
[1387] "268465"    "268491"    "268591"    "268697"    "268755"    "268860"   
[1393] "268903"    "268930"    "269254"    "269275"    "269610"    "269682"   
[1399] "269701"    "270624"    "271036"    "271127"    "271564"    "271639"   
[1405] "272643"    "276920"    "278240"    "280287"    "280667"    "280668"   
[1411] "317653"    "319177"    "319448"    "319953"    "320022"    "320244"   
[1417] "320277"    "320558"    "320752"    "320790"    "327826"    "328019"   
[1423] "328365"    "328401"    "328440"    "328580"    "328845"    "329557"   
[1429] "329954"    "330149"    "330188"    "330319"    "330409"    "330470"   
[1435] "330830"    "330890"    "331046"    "331416"    "332110"    "332397"   
[1441] "353188"    "378430"    "378462"    "380654"    "380684"    "380702"   
[1447] "380709"    "380773"    "380855"    "380993"    "380994"    "381022"   
[1453] "381157"    "381196"    "381290"    "381404"    "381489"    "381677"   
[1459] "381678"    "381759"    "382007"    "382077"    "382217"    "382275"   
[1465] "382277"    "382301"    "383491"    "384619"    "384806"    "384813"   
[1471] "387139"    "387140"    "387153"    "387156"    "387161"    "387162"   
[1477] "387177"    "387178"    "387179"    "387188"    "387198"    "387218"   
[1483] "387244"    "387245"    "387246"    "387247"    "399599"    "433700"   
[1489] "434438"    "434768"    "434784"    "434794"    "442829"    "544736"   
[1495] "545156"    "546055"    "546118"    "546272"    "546282"    "574428"   
[1501] "574437"    "574438"    "619517"    "619697"    "619991"    "622480"   
[1507] "622554"    "623474"    "625249"    "625662"    "627081"    "628438"   
[1513] "637277"    "664799"    "664829"    "665270"    "665780"    "666317"   
[1519] "666528"    "668110"    "668929"    "671232"    "671564"    "723849"   
[1525] "723868"    "723886"    "723932"    "723939"    "723955"    "723956"   
[1531] "723962"    "723965"    "723966"    "735262"    "735309"    "751535"   
[1537] "100009600" "100038417" "100038489" "100038977" "100039030" "100039065"
[1543] "100039120" "100039842" "100039905" "100040608" "100040894" "100042109"
[1549] "100042175" "100042922" "100042929" "100042931" "100042939" "100042943"
[1555] "100042944" "100042946" "100043216" "100048534" "100049545" "100049546"
[1561] "100049548" "100113365" "100124460" "100124479" "100124480" "100190765"
[1567] "100270744" "100503361" "100504642" "100861637" "100861881" "101055773"
[1573] "101056116" "101056210" "102443351" "102631559" "102633564" "102636501"
[1579] "102638101" "102638793" "102639094" "102639490" "102639895" "105247282"
[1585] "108168511" "108168530" "108168552" "108168557" "108168582" "108168594"
[1591] "113523646"

$`GO:0000012`
 [1] "11545"  "14211"  "22064"  "22594"  "66408"  "70099"  "71991"  "72103" 
 [9] "93759"  "104884" "319583" "319955"

> # 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:0002282                5                 5        1.6379883  0.0001089845
GO:0019886               16                16        1.0776253  0.0002145139
GO:1905146               17                17        1.0606304  0.0002244091
GO:1900424               17                15        1.0721442  0.0003038984
GO:1900426               12                10        1.1666016  0.0004664378
GO:0002495               21                21        0.9671930  0.0004860756
GO:0002478               27                26        0.9072525  0.0005366052
GO:0007039               19                19        0.9829004  0.0005518269
GO:0002504               22                22        0.9409343  0.0006380768
GO:0140059               10                 9        1.1540213  0.0008533323
                                                                                  geneSetDescription
GO:0002282                                    microglial cell activation involved in immune response
GO:0019886         antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:1905146                                                       lysosomal protein catabolic process
GO:1900424                                               regulation of defense response to bacterium
GO:1900426                                      positive regulation of defense response to bacterium
GO:0002495                   antigen processing and presentation of peptide antigen via MHC class II
GO:0002478                          antigen processing and presentation of exogenous peptide antigen
GO:0007039                                                  protein catabolic process in the vacuole
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
GO:0140059                                                                     dendrite arborization
> # output changes with annotation version !
> 
> plotGOgraph(object = mlpObject, main = "test of main")
Loading required namespace: Rgraphviz
Loading required namespace: GOstats
Loading required namespace: gplots
> 
> 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 
  44.29    1.56   45.84 

Example timings

MLP.Rcheck/examples_i386/MLP-Ex.timings

nameusersystemelapsed
MLP22.32 1.6524.08
addGeneSetDescription55.43 4.3359.76
getGeneSets66.53 5.0694.42
mlpBarplot0.080.000.11
plot.MLP2.800.082.88
plotGOgraph0.510.020.53
plotGeneSetSignificance0.610.060.69

MLP.Rcheck/examples_x64/MLP-Ex.timings

nameusersystemelapsed
MLP20.67 0.3321.00
addGeneSetDescription52.05 1.1553.22
getGeneSets68.08 0.7889.58
mlpBarplot0.060.000.06
plot.MLP2.250.182.42
plotGOgraph0.430.030.46
plotGeneSetSignificance0.500.010.52