Tobias Verbeke
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/MLP |
| git_branch: RELEASE_3_14 |
| git_last_commit: 6946b4f |
| git_last_commit_date: 2021-10-26 11:57:36 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:55 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
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 reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1180/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MLP 1.42.0 (landing page) Tobias Verbeke
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MLP |
| Version: 1.42.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLP.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MLP_1.42.0.tar.gz |
| StartedAt: 2022-04-12 23:04:08 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 23:17:55 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 826.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MLP.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MLP.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MLP_1.42.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MLP.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.42.0'
* 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 69.03 3.01 102.98
addGeneSetDescription 55.78 3.75 81.09
MLP 19.39 1.05 20.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getGeneSets 67.37 0.96 91.72
addGeneSetDescription 50.92 1.58 52.50
MLP 19.83 0.67 20.53
* 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
MLP.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MLP_1.42.0.tar.gz && rm -rf MLP.buildbin-libdir && mkdir MLP.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MLP.buildbin-libdir MLP_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MLP_1.42.0.zip && rm MLP_1.42.0.tar.gz MLP_1.42.0.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
18 4107k 18 772k 0 0 830k 0 0:00:04 --:--:-- 0:00:04 830k
61 4107k 61 2525k 0 0 1310k 0 0:00:03 0:00:01 0:00:02 1310k
100 4107k 100 4107k 0 0 1608k 0 0:00:02 0:00:02 --:--:-- 1609k
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_1.42.0.zip
* DONE (MLP)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MLP' successfully unpacked and MD5 sums checked
|
MLP.Rcheck/tests_i386/test.KEGG.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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
48.54 0.78 73.22
>
> 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
55.89 1.65 102.70
|
MLP.Rcheck/tests_x64/test.KEGG.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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
52.68 0.69 77.61
>
> 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
59.21 1.65 105.98
|
|
MLP.Rcheck/tests_i386/test.MLP.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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
Attaching package: 'BiocGenerics'
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
25.29 3.61 28.90
> 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" "13121" "13123" "13134"
[157] "13164" "13166" "13205" "13206" "13214" "13363"
[163] "13382" "13383" "13393" "13404" "13411" "13435"
[169] "13487" "13488" "13491" "13492" "13498" "13524"
[175] "13525" "13526" "13529" "13614" "13615" "13617"
[181] "13618" "13649" "13653" "13667" "13731" "13813"
[187] "13819" "13852" "13854" "13856" "13857" "13866"
[193] "13870" "13874" "13875" "13982" "13983" "13984"
[199] "14008" "14011" "14087" "14088" "14155" "14160"
[205] "14165" "14178" "14179" "14180" "14183" "14211"
[211] "14228" "14238" "14275" "14276" "14283" "14308"
[217] "14309" "14313" "14347" "14366" "14367" "14388"
[223] "14402" "14421" "14425" "14431" "14447" "14453"
[229] "14460" "14461" "14462" "14463" "14531" "14536"
[235] "14566" "14595" "14598" "14609" "14610" "14620"
[241] "14622" "14632" "14633" "14654" "14658" "14682"
[247] "14705" "14714" "14725" "14748" "14764" "14766"
[253] "14782" "14784" "14810" "14815" "14824" "15013"
[259] "15018" "15078" "15081" "15110" "15170" "15182"
[265] "15194" "15204" "15205" "15209" "15211" "15212"
[271] "15213" "15214" "15221" "15235" "15247" "15251"
[277] "15270" "15361" "15364" "15373" "15375" "15377"
[283] "15378" "15387" "15395" "15396" "15398" "15405"
[289] "15408" "15423" "15430" "15431" "15433" "15438"
[295] "15446" "15463" "15482" "15484" "15486" "15487"
[301] "15488" "15499" "15500" "15502" "15511" "15512"
[307] "15516" "15567" "15570" "15574" "15894" "15904"
[313] "16000" "16001" "16002" "16007" "16011" "16147"
[319] "16153" "16157" "16173" "16175" "16176" "16319"
[325] "16322" "16323" "16324" "16330" "16336" "16337"
[331] "16365" "16401" "16410" "16412" "16433" "16450"
[337] "16477" "16532" "16542" "16590" "16601" "16650"
[343] "16669" "16691" "16777" "16783" "16833" "16842"
[349] "16846" "16847" "16848" "16859" "16866" "16867"
[355] "16869" "16871" "16872" "16875" "16876" "16878"
[361] "16886" "16952" "16970" "16974" "17125" "17128"
[367] "17129" "17149" "17171" "17173" "17191" "17221"
[373] "17235" "17240" "17242" "17256" "17283" "17289"
[379] "17295" "17300" "17304" "17311" "17345" "17350"
[385] "17381" "17390" "17395" "17427" "17450" "17451"
[391] "17535" "17684" "17685" "17686" "17687" "17688"
[397] "17701" "17702" "17761" "17771" "17776" "17836"
[403] "17864" "17886" "17977" "17978" "17979" "17986"
[409] "18000" "18004" "18005" "18011" "18014" "18022"
[415] "18072" "18095" "18119" "18121" "18127" "18128"
[421] "18129" "18142" "18159" "18168" "18194" "18211"
[427] "18285" "18286" "18291" "18292" "18387" "18413"
[433] "18417" "18426" "18429" "18430" "18431" "18436"
[439] "18441" "18442" "18472" "18475" "18476" "18504"
[445] "18507" "18514" "18551" "18552" "18555" "18591"
[451] "18595" "18606" "18617" "18663" "18667" "18671"
[457] "18747" "18749" "18763" "18764" "18766" "18775"
[463] "18776" "18783" "18787" "18791" "18792" "18793"
[469] "18795" "18799" "18802" "18811" "18812" "18814"
[475] "18815" "18817" "18830" "18858" "18861" "18952"
[481] "19014" "19015" "19016" "19049" "19052" "19059"
[487] "19090" "19109" "19110" "19111" "19112" "19113"
[493] "19114" "19116" "19118" "19119" "19120" "19143"
[499] "19156" "19183" "19204" "19211" "19214" "19215"
[505] "19219" "19223" "19225" "19229" "19242" "19247"
[511] "19275" "19288" "19294" "19317" "19339" "19353"
[517] "19355" "19357" "19359" "19360" "19361" "19362"
[523] "19364" "19366" "19401" "19411" "19662" "19664"
[529] "19701" "19725" "19733" "19735" "19773" "19821"
[535] "19886" "20017" "20104" "20112" "20181" "20182"
[541] "20315" "20317" "20319" "20322" "20346" "20363"
[547] "20377" "20397" "20415" "20423" "20437" "20473"
[553] "20474" "20475" "20520" "20541" "20613" "20655"
[559] "20662" "20670" "20671" "20674" "20675" "20681"
[565] "20682" "20683" "20686" "20687" "20690" "20708"
[571] "20719" "20720" "20724" "20729" "20730" "20732"
[577] "20733" "20744" "20758" "20779" "20826" "20843"
[583] "20848" "20850" "20851" "20860" "20869" "20871"
[589] "20873" "20878" "20892" "20897" "20899" "20905"
[595] "20910" "20957" "20962" "20997" "21333" "21334"
[601] "21336" "21337" "21338" "21357" "21386" "21405"
[607] "21410" "21412" "21414" "21416" "21425" "21454"
[613] "21463" "21645" "21674" "21679" "21744" "21749"
[619] "21803" "21808" "21812" "21821" "21823" "21824"
[625] "21830" "21833" "21834" "21843" "21849" "21857"
[631] "21869" "21887" "21923" "21945" "21958" "21959"
[637] "21973" "21974" "22022" "22026" "22061" "22064"
[643] "22065" "22068" "22092" "22113" "22114" "22115"
[649] "22127" "22137" "22174" "22187" "22209" "22210"
[655] "22215" "22249" "22329" "22334" "22337" "22339"
[661] "22353" "22371" "22384" "22412" "22413" "22415"
[667] "22417" "22418" "22421" "22422" "22431" "22441"
[673] "22445" "22446" "22589" "22632" "22635" "22661"
[679] "22668" "22691" "22694" "22696" "22697" "22698"
[685] "22701" "22702" "22715" "22762" "22764" "22768"
[691] "22786" "22787" "22788" "22789" "23793" "23885"
[697] "23887" "23920" "23950" "23967" "23968" "23980"
[703] "23991" "23997" "24061" "24084" "24086" "24127"
[709] "24128" "26357" "26362" "26366" "26370" "26380"
[715] "26384" "26395" "26407" "26413" "26416" "26417"
[721] "26423" "26434" "26437" "26564" "26565" "26900"
[727] "26909" "26910" "26920" "26927" "26934" "26942"
[733] "26946" "26972" "27061" "27083" "27084" "27206"
[739] "27222" "27354" "27356" "27372" "27386" "28036"
[745] "28078" "28088" "28105" "28114" "28135" "29871"
[751] "29876" "30054" "30841" "30939" "30953" "30959"
[757] "50500" "50501" "50505" "50525" "50722" "50785"
[763] "50790" "50796" "50878" "50915" "51789" "51792"
[769] "51885" "51938" "52020" "52028" "52679" "52683"
[775] "52864" "53381" "53419" "53422" "53424" "53601"
[781] "53604" "53614" "53814" "53878" "53885" "53897"
[787] "53975" "54003" "54004" "54137" "54140" "54204"
[793] "54352" "54383" "54388" "54418" "54427" "54486"
[799] "54524" "54562" "54608" "54611" "54650" "54725"
[805] "55925" "55978" "55993" "55994" "56092" "56094"
[811] "56096" "56213" "56218" "56223" "56228" "56274"
[817] "56291" "56296" "56312" "56334" "56335" "56371"
[823] "56406" "56436" "56449" "56484" "56503" "56523"
[829] "56526" "56622" "56635" "56693" "56710" "56711"
[835] "56717" "56739" "56746" "57256" "57264" "57320"
[841] "57746" "57749" "57815" "57816" "57908" "58186"
[847] "58226" "58230" "58231" "58864" "58991" "58998"
[853] "59030" "59083" "60530" "60534" "60597" "60611"
[859] "63872" "64009" "64335" "64383" "64707" "64931"
[865] "65247" "65971" "66193" "66197" "66313" "66392"
[871] "66515" "66573" "66634" "66654" "66707" "66712"
[877] "66713" "66720" "66722" "66793" "66826" "66923"
[883] "66977" "66983" "67000" "67010" "67030" "67042"
[889] "67052" "67077" "67121" "67141" "67181" "67204"
[895] "67231" "67310" "67331" "67333" "67345" "67374"
[901] "67378" "67402" "67504" "67505" "67537" "67555"
[907] "67561" "67652" "67690" "67713" "67753" "67869"
[913] "67909" "67946" "67968" "67971" "67981" "68107"
[919] "68166" "68170" "68231" "68265" "68275" "68298"
[925] "68328" "68549" "68708" "68767" "68911" "68922"
[931] "68981" "69032" "69064" "69260" "69286" "69287"
[937] "69306" "69307" "69310" "69329" "69376" "69444"
[943] "69538" "69546" "69707" "69716" "69852" "69865"
[949] "69928" "69940" "69982" "70069" "70093" "70099"
[955] "70231" "70235" "70248" "70375" "70441" "70465"
[961] "70503" "70691" "70772" "70840" "70862" "70873"
[967] "70891" "70918" "70956" "70977" "71037" "71062"
[973] "71089" "71099" "71132" "71175" "71233" "71241"
[979] "71242" "71371" "71567" "71709" "71711" "71765"
[985] "71830" "71836" "71840" "71841" "71846" "71860"
[991] "71870" "71904" "71914" "71950" "71981" "72135"
[997] "72148" "72162" "72236" "72415" "72469" "72504"
[1003] "72508" "72568" "72634" "72780" "72787" "72891"
[1009] "72938" "73242" "73244" "73296" "73316" "73329"
[1015] "73333" "73336" "73412" "73456" "73472" "73542"
[1021] "73616" "73673" "73677" "73679" "73721" "74041"
[1027] "74052" "74068" "74075" "74090" "74117" "74174"
[1033] "74188" "74222" "74229" "74237" "74267" "74286"
[1039] "74288" "74297" "74309" "74354" "74360" "74369"
[1045] "74377" "74383" "74386" "74401" "74434" "74446"
[1051] "74450" "74453" "74468" "74469" "74666" "74691"
[1057] "74708" "74711" "74716" "74754" "74847" "74927"
[1063] "75002" "75019" "75033" "75140" "75178" "75202"
[1069] "75388" "75410" "75437" "75459" "75469" "75514"
[1075] "75533" "75571" "75596" "75605" "75622" "75642"
[1081] "75646" "75753" "75801" "75826" "75828" "75909"
[1087] "76378" "76407" "76421" "76457" "76486" "76499"
[1093] "76573" "76606" "76718" "76800" "76850" "76856"
[1099] "76858" "76867" "76915" "76925" "76943" "77053"
[1105] "77128" "77254" "77424" "77595" "77609" "77963"
[1111] "77980" "78081" "78118" "78124" "78284" "78619"
[1117] "78634" "78658" "78784" "78801" "78803" "78925"
[1123] "79459" "80297" "80517" "80838" "80884" "80912"
[1129] "81018" "83434" "83456" "83557" "83558" "83560"
[1135] "83561" "83964" "83984" "93670" "93684" "93736"
[1141] "93757" "93759" "93760" "93837" "93960" "94109"
[1147] "94221" "94224" "94244" "94246" "97086" "97165"
[1153] "98558" "98711" "99412" "99929" "100121" "100155"
[1159] "100317" "100535" "100986" "101100" "101187" "101476"
[1165] "102774" "102991" "103468" "103554" "103583" "103733"
[1171] "103768" "104083" "104111" "104148" "104156" "104263"
[1177] "104271" "104310" "104346" "104362" "104601" "104799"
[1183] "104806" "105349" "105511" "105988" "106389" "106757"
[1189] "107515" "107586" "107626" "107656" "107849" "107970"
[1195] "107995" "108829" "108961" "109685" "109689" "109727"
[1201] "109785" "110012" "110082" "110084" "110147" "110355"
[1207] "110459" "110542" "110957" "110958" "112405" "114602"
[1213] "114606" "114642" "114661" "114662" "114714" "114875"
[1219] "116837" "140498" "140557" "170676" "170731" "171285"
[1225] "171429" "171506" "192119" "192176" "192195" "192199"
[1231] "192236" "192897" "193322" "193838" "194908" "195434"
[1237] "207165" "207182" "207304" "207352" "207607" "207686"
[1243] "208144" "208169" "208188" "208727" "209011" "209091"
[1249] "210510" "210529" "210554" "211064" "211484" "211651"
[1255] "212517" "212670" "212937" "213081" "213236" "213272"
[1261] "213389" "213402" "213541" "213742" "214105" "214253"
[1267] "214290" "214292" "214321" "214384" "214572" "214575"
[1273] "214593" "214901" "215028" "215029" "215095" "215387"
[1279] "215854" "216350" "216725" "216869" "217039" "217116"
[1285] "217216" "217325" "217341" "217715" "217716" "218214"
[1291] "218454" "219038" "223593" "223697" "223825" "223921"
[1297] "223989" "224045" "224171" "224661" "224727" "224826"
[1303] "224902" "225182" "225497" "225865" "226049" "226090"
[1309] "226162" "226265" "226841" "227210" "227394" "227615"
[1315] "227631" "227736" "228421" "228980" "229096" "229227"
[1321] "229357" "229700" "229841" "230103" "230126" "230594"
[1327] "230700" "230809" "230861" "230899" "231051" "231386"
[1333] "231600" "231633" "231672" "231832" "231912" "232174"
[1339] "232223" "232286" "232345" "232664" "232816" "233276"
[1345] "234857" "235072" "235320" "235330" "235345" "235380"
[1351] "235559" "235626" "235628" "235682" "236266" "236899"
[1357] "237336" "237625" "237911" "238055" "238057" "238247"
[1363] "238328" "238330" "238405" "238406" "239083" "239167"
[1369] "239528" "239731" "240069" "240255" "240590" "240697"
[1375] "240725" "240899" "241116" "241296" "241516" "241624"
[1381] "242202" "242523" "242620" "243862" "243866" "243897"
[1387] "243905" "244486" "244495" "244551" "245000" "245865"
[1393] "246747" "252828" "252866" "252868" "252967" "252973"
[1399] "259279" "260305" "263876" "264134" "268396" "268420"
[1405] "268465" "268491" "268591" "268697" "268755" "268860"
[1411] "268903" "268930" "269254" "269275" "269610" "269682"
[1417] "269701" "270624" "271036" "271127" "271564" "271639"
[1423] "272643" "276920" "278240" "280287" "280667" "280668"
[1429] "317653" "319177" "319448" "319953" "320022" "320244"
[1435] "320256" "320277" "320558" "320752" "320790" "320878"
[1441] "327826" "328019" "328365" "328401" "328440" "328580"
[1447] "328845" "329557" "329954" "330149" "330188" "330319"
[1453] "330409" "330470" "330830" "330890" "331046" "331416"
[1459] "331537" "332110" "332397" "353188" "353204" "378430"
[1465] "378462" "380654" "380684" "380702" "380709" "380773"
[1471] "380855" "380993" "380994" "381022" "381157" "381196"
[1477] "381218" "381229" "381290" "381404" "381489" "381677"
[1483] "381678" "381759" "382007" "382077" "382113" "382217"
[1489] "382275" "382277" "382301" "383491" "384619" "384806"
[1495] "384813" "387139" "387140" "387153" "387156" "387161"
[1501] "387162" "387177" "387178" "387179" "387188" "387198"
[1507] "387218" "387244" "387245" "387246" "387247" "399599"
[1513] "433700" "434438" "434768" "434784" "434794" "442829"
[1519] "544736" "545156" "546055" "546118" "546272" "546282"
[1525] "574428" "574437" "574438" "619517" "619697" "619991"
[1531] "622480" "622554" "623474" "625249" "625662" "627081"
[1537] "628438" "637277" "664799" "664829" "665270" "665780"
[1543] "666317" "666528" "668110" "668929" "671232" "671564"
[1549] "723849" "723868" "723886" "723932" "723939" "723955"
[1555] "723956" "723962" "723965" "723966" "735262" "735309"
[1561] "751535" "100009600" "100038417" "100038489" "100038977" "100039030"
[1567] "100039065" "100039120" "100039842" "100039905" "100040608" "100040894"
[1573] "100042109" "100042175" "100042922" "100042929" "100042931" "100042939"
[1579] "100042943" "100042944" "100042946" "100043216" "100048534" "100049545"
[1585] "100049546" "100049548" "100113365" "100124460" "100124479" "100124480"
[1591] "100190765" "100270744" "100503361" "100504642" "100861637" "100861881"
[1597] "101055773" "101056116" "101056210" "102443351" "102631559" "102632837"
[1603] "102633564" "102636501" "102638101" "102638793" "102639094" "102639490"
[1609] "102639895" "105247282" "108168511" "108168530" "108168552" "108168557"
[1615] "108168582" "108168594" "113523646" "118451630"
$`GO:0000012`
[1] "11545" "14211" "21958" "22064" "22594" "66408" "70099" "71991"
[9] "72103" "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 8.990006e-05
GO:0019886 20 18 1.0842469 1.303508e-04
GO:1905146 17 17 1.0606304 2.546313e-04
GO:1900424 18 16 1.0750521 2.599783e-04
GO:0002495 24 22 0.9910381 2.629097e-04
GO:0070900 5 5 1.4404406 5.299527e-04
GO:1900864 5 5 1.4404406 5.299527e-04
GO:0002504 26 24 0.9261644 5.672125e-04
GO:0007039 19 19 0.9829004 5.924932e-04
GO:1900426 12 10 1.1666016 5.978555e-04
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:0002495 antigen processing and presentation of peptide antigen via MHC class II
GO:0070900 mitochondrial tRNA modification
GO:1900864 mitochondrial RNA modification
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
GO:0007039 protein catabolic process in the vacuole
GO:1900426 positive regulation of defense response to bacterium
> # 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
45.82 3.98 49.92
|
MLP.Rcheck/tests_x64/test.MLP.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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
Attaching package: 'BiocGenerics'
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
29.2 1.3 30.5
> 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" "13121" "13123" "13134"
[157] "13164" "13166" "13205" "13206" "13214" "13363"
[163] "13382" "13383" "13393" "13404" "13411" "13435"
[169] "13487" "13488" "13491" "13492" "13498" "13524"
[175] "13525" "13526" "13529" "13614" "13615" "13617"
[181] "13618" "13649" "13653" "13667" "13731" "13813"
[187] "13819" "13852" "13854" "13856" "13857" "13866"
[193] "13870" "13874" "13875" "13982" "13983" "13984"
[199] "14008" "14011" "14087" "14088" "14155" "14160"
[205] "14165" "14178" "14179" "14180" "14183" "14211"
[211] "14228" "14238" "14275" "14276" "14283" "14308"
[217] "14309" "14313" "14347" "14366" "14367" "14388"
[223] "14402" "14421" "14425" "14431" "14447" "14453"
[229] "14460" "14461" "14462" "14463" "14531" "14536"
[235] "14566" "14595" "14598" "14609" "14610" "14620"
[241] "14622" "14632" "14633" "14654" "14658" "14682"
[247] "14705" "14714" "14725" "14748" "14764" "14766"
[253] "14782" "14784" "14810" "14815" "14824" "15013"
[259] "15018" "15078" "15081" "15110" "15170" "15182"
[265] "15194" "15204" "15205" "15209" "15211" "15212"
[271] "15213" "15214" "15221" "15235" "15247" "15251"
[277] "15270" "15361" "15364" "15373" "15375" "15377"
[283] "15378" "15387" "15395" "15396" "15398" "15405"
[289] "15408" "15423" "15430" "15431" "15433" "15438"
[295] "15446" "15463" "15482" "15484" "15486" "15487"
[301] "15488" "15499" "15500" "15502" "15511" "15512"
[307] "15516" "15567" "15570" "15574" "15894" "15904"
[313] "16000" "16001" "16002" "16007" "16011" "16147"
[319] "16153" "16157" "16173" "16175" "16176" "16319"
[325] "16322" "16323" "16324" "16330" "16336" "16337"
[331] "16365" "16401" "16410" "16412" "16433" "16450"
[337] "16477" "16532" "16542" "16590" "16601" "16650"
[343] "16669" "16691" "16777" "16783" "16833" "16842"
[349] "16846" "16847" "16848" "16859" "16866" "16867"
[355] "16869" "16871" "16872" "16875" "16876" "16878"
[361] "16886" "16952" "16970" "16974" "17125" "17128"
[367] "17129" "17149" "17171" "17173" "17191" "17221"
[373] "17235" "17240" "17242" "17256" "17283" "17289"
[379] "17295" "17300" "17304" "17311" "17345" "17350"
[385] "17381" "17390" "17395" "17427" "17450" "17451"
[391] "17535" "17684" "17685" "17686" "17687" "17688"
[397] "17701" "17702" "17761" "17771" "17776" "17836"
[403] "17864" "17886" "17977" "17978" "17979" "17986"
[409] "18000" "18004" "18005" "18011" "18014" "18022"
[415] "18072" "18095" "18119" "18121" "18127" "18128"
[421] "18129" "18142" "18159" "18168" "18194" "18211"
[427] "18285" "18286" "18291" "18292" "18387" "18413"
[433] "18417" "18426" "18429" "18430" "18431" "18436"
[439] "18441" "18442" "18472" "18475" "18476" "18504"
[445] "18507" "18514" "18551" "18552" "18555" "18591"
[451] "18595" "18606" "18617" "18663" "18667" "18671"
[457] "18747" "18749" "18763" "18764" "18766" "18775"
[463] "18776" "18783" "18787" "18791" "18792" "18793"
[469] "18795" "18799" "18802" "18811" "18812" "18814"
[475] "18815" "18817" "18830" "18858" "18861" "18952"
[481] "19014" "19015" "19016" "19049" "19052" "19059"
[487] "19090" "19109" "19110" "19111" "19112" "19113"
[493] "19114" "19116" "19118" "19119" "19120" "19143"
[499] "19156" "19183" "19204" "19211" "19214" "19215"
[505] "19219" "19223" "19225" "19229" "19242" "19247"
[511] "19275" "19288" "19294" "19317" "19339" "19353"
[517] "19355" "19357" "19359" "19360" "19361" "19362"
[523] "19364" "19366" "19401" "19411" "19662" "19664"
[529] "19701" "19725" "19733" "19735" "19773" "19821"
[535] "19886" "20017" "20104" "20112" "20181" "20182"
[541] "20315" "20317" "20319" "20322" "20346" "20363"
[547] "20377" "20397" "20415" "20423" "20437" "20473"
[553] "20474" "20475" "20520" "20541" "20613" "20655"
[559] "20662" "20670" "20671" "20674" "20675" "20681"
[565] "20682" "20683" "20686" "20687" "20690" "20708"
[571] "20719" "20720" "20724" "20729" "20730" "20732"
[577] "20733" "20744" "20758" "20779" "20826" "20843"
[583] "20848" "20850" "20851" "20860" "20869" "20871"
[589] "20873" "20878" "20892" "20897" "20899" "20905"
[595] "20910" "20957" "20962" "20997" "21333" "21334"
[601] "21336" "21337" "21338" "21357" "21386" "21405"
[607] "21410" "21412" "21414" "21416" "21425" "21454"
[613] "21463" "21645" "21674" "21679" "21744" "21749"
[619] "21803" "21808" "21812" "21821" "21823" "21824"
[625] "21830" "21833" "21834" "21843" "21849" "21857"
[631] "21869" "21887" "21923" "21945" "21958" "21959"
[637] "21973" "21974" "22022" "22026" "22061" "22064"
[643] "22065" "22068" "22092" "22113" "22114" "22115"
[649] "22127" "22137" "22174" "22187" "22209" "22210"
[655] "22215" "22249" "22329" "22334" "22337" "22339"
[661] "22353" "22371" "22384" "22412" "22413" "22415"
[667] "22417" "22418" "22421" "22422" "22431" "22441"
[673] "22445" "22446" "22589" "22632" "22635" "22661"
[679] "22668" "22691" "22694" "22696" "22697" "22698"
[685] "22701" "22702" "22715" "22762" "22764" "22768"
[691] "22786" "22787" "22788" "22789" "23793" "23885"
[697] "23887" "23920" "23950" "23967" "23968" "23980"
[703] "23991" "23997" "24061" "24084" "24086" "24127"
[709] "24128" "26357" "26362" "26366" "26370" "26380"
[715] "26384" "26395" "26407" "26413" "26416" "26417"
[721] "26423" "26434" "26437" "26564" "26565" "26900"
[727] "26909" "26910" "26920" "26927" "26934" "26942"
[733] "26946" "26972" "27061" "27083" "27084" "27206"
[739] "27222" "27354" "27356" "27372" "27386" "28036"
[745] "28078" "28088" "28105" "28114" "28135" "29871"
[751] "29876" "30054" "30841" "30939" "30953" "30959"
[757] "50500" "50501" "50505" "50525" "50722" "50785"
[763] "50790" "50796" "50878" "50915" "51789" "51792"
[769] "51885" "51938" "52020" "52028" "52679" "52683"
[775] "52864" "53381" "53419" "53422" "53424" "53601"
[781] "53604" "53614" "53814" "53878" "53885" "53897"
[787] "53975" "54003" "54004" "54137" "54140" "54204"
[793] "54352" "54383" "54388" "54418" "54427" "54486"
[799] "54524" "54562" "54608" "54611" "54650" "54725"
[805] "55925" "55978" "55993" "55994" "56092" "56094"
[811] "56096" "56213" "56218" "56223" "56228" "56274"
[817] "56291" "56296" "56312" "56334" "56335" "56371"
[823] "56406" "56436" "56449" "56484" "56503" "56523"
[829] "56526" "56622" "56635" "56693" "56710" "56711"
[835] "56717" "56739" "56746" "57256" "57264" "57320"
[841] "57746" "57749" "57815" "57816" "57908" "58186"
[847] "58226" "58230" "58231" "58864" "58991" "58998"
[853] "59030" "59083" "60530" "60534" "60597" "60611"
[859] "63872" "64009" "64335" "64383" "64707" "64931"
[865] "65247" "65971" "66193" "66197" "66313" "66392"
[871] "66515" "66573" "66634" "66654" "66707" "66712"
[877] "66713" "66720" "66722" "66793" "66826" "66923"
[883] "66977" "66983" "67000" "67010" "67030" "67042"
[889] "67052" "67077" "67121" "67141" "67181" "67204"
[895] "67231" "67310" "67331" "67333" "67345" "67374"
[901] "67378" "67402" "67504" "67505" "67537" "67555"
[907] "67561" "67652" "67690" "67713" "67753" "67869"
[913] "67909" "67946" "67968" "67971" "67981" "68107"
[919] "68166" "68170" "68231" "68265" "68275" "68298"
[925] "68328" "68549" "68708" "68767" "68911" "68922"
[931] "68981" "69032" "69064" "69260" "69286" "69287"
[937] "69306" "69307" "69310" "69329" "69376" "69444"
[943] "69538" "69546" "69707" "69716" "69852" "69865"
[949] "69928" "69940" "69982" "70069" "70093" "70099"
[955] "70231" "70235" "70248" "70375" "70441" "70465"
[961] "70503" "70691" "70772" "70840" "70862" "70873"
[967] "70891" "70918" "70956" "70977" "71037" "71062"
[973] "71089" "71099" "71132" "71175" "71233" "71241"
[979] "71242" "71371" "71567" "71709" "71711" "71765"
[985] "71830" "71836" "71840" "71841" "71846" "71860"
[991] "71870" "71904" "71914" "71950" "71981" "72135"
[997] "72148" "72162" "72236" "72415" "72469" "72504"
[1003] "72508" "72568" "72634" "72780" "72787" "72891"
[1009] "72938" "73242" "73244" "73296" "73316" "73329"
[1015] "73333" "73336" "73412" "73456" "73472" "73542"
[1021] "73616" "73673" "73677" "73679" "73721" "74041"
[1027] "74052" "74068" "74075" "74090" "74117" "74174"
[1033] "74188" "74222" "74229" "74237" "74267" "74286"
[1039] "74288" "74297" "74309" "74354" "74360" "74369"
[1045] "74377" "74383" "74386" "74401" "74434" "74446"
[1051] "74450" "74453" "74468" "74469" "74666" "74691"
[1057] "74708" "74711" "74716" "74754" "74847" "74927"
[1063] "75002" "75019" "75033" "75140" "75178" "75202"
[1069] "75388" "75410" "75437" "75459" "75469" "75514"
[1075] "75533" "75571" "75596" "75605" "75622" "75642"
[1081] "75646" "75753" "75801" "75826" "75828" "75909"
[1087] "76378" "76407" "76421" "76457" "76486" "76499"
[1093] "76573" "76606" "76718" "76800" "76850" "76856"
[1099] "76858" "76867" "76915" "76925" "76943" "77053"
[1105] "77128" "77254" "77424" "77595" "77609" "77963"
[1111] "77980" "78081" "78118" "78124" "78284" "78619"
[1117] "78634" "78658" "78784" "78801" "78803" "78925"
[1123] "79459" "80297" "80517" "80838" "80884" "80912"
[1129] "81018" "83434" "83456" "83557" "83558" "83560"
[1135] "83561" "83964" "83984" "93670" "93684" "93736"
[1141] "93757" "93759" "93760" "93837" "93960" "94109"
[1147] "94221" "94224" "94244" "94246" "97086" "97165"
[1153] "98558" "98711" "99412" "99929" "100121" "100155"
[1159] "100317" "100535" "100986" "101100" "101187" "101476"
[1165] "102774" "102991" "103468" "103554" "103583" "103733"
[1171] "103768" "104083" "104111" "104148" "104156" "104263"
[1177] "104271" "104310" "104346" "104362" "104601" "104799"
[1183] "104806" "105349" "105511" "105988" "106389" "106757"
[1189] "107515" "107586" "107626" "107656" "107849" "107970"
[1195] "107995" "108829" "108961" "109685" "109689" "109727"
[1201] "109785" "110012" "110082" "110084" "110147" "110355"
[1207] "110459" "110542" "110957" "110958" "112405" "114602"
[1213] "114606" "114642" "114661" "114662" "114714" "114875"
[1219] "116837" "140498" "140557" "170676" "170731" "171285"
[1225] "171429" "171506" "192119" "192176" "192195" "192199"
[1231] "192236" "192897" "193322" "193838" "194908" "195434"
[1237] "207165" "207182" "207304" "207352" "207607" "207686"
[1243] "208144" "208169" "208188" "208727" "209011" "209091"
[1249] "210510" "210529" "210554" "211064" "211484" "211651"
[1255] "212517" "212670" "212937" "213081" "213236" "213272"
[1261] "213389" "213402" "213541" "213742" "214105" "214253"
[1267] "214290" "214292" "214321" "214384" "214572" "214575"
[1273] "214593" "214901" "215028" "215029" "215095" "215387"
[1279] "215854" "216350" "216725" "216869" "217039" "217116"
[1285] "217216" "217325" "217341" "217715" "217716" "218214"
[1291] "218454" "219038" "223593" "223697" "223825" "223921"
[1297] "223989" "224045" "224171" "224661" "224727" "224826"
[1303] "224902" "225182" "225497" "225865" "226049" "226090"
[1309] "226162" "226265" "226841" "227210" "227394" "227615"
[1315] "227631" "227736" "228421" "228980" "229096" "229227"
[1321] "229357" "229700" "229841" "230103" "230126" "230594"
[1327] "230700" "230809" "230861" "230899" "231051" "231386"
[1333] "231600" "231633" "231672" "231832" "231912" "232174"
[1339] "232223" "232286" "232345" "232664" "232816" "233276"
[1345] "234857" "235072" "235320" "235330" "235345" "235380"
[1351] "235559" "235626" "235628" "235682" "236266" "236899"
[1357] "237336" "237625" "237911" "238055" "238057" "238247"
[1363] "238328" "238330" "238405" "238406" "239083" "239167"
[1369] "239528" "239731" "240069" "240255" "240590" "240697"
[1375] "240725" "240899" "241116" "241296" "241516" "241624"
[1381] "242202" "242523" "242620" "243862" "243866" "243897"
[1387] "243905" "244486" "244495" "244551" "245000" "245865"
[1393] "246747" "252828" "252866" "252868" "252967" "252973"
[1399] "259279" "260305" "263876" "264134" "268396" "268420"
[1405] "268465" "268491" "268591" "268697" "268755" "268860"
[1411] "268903" "268930" "269254" "269275" "269610" "269682"
[1417] "269701" "270624" "271036" "271127" "271564" "271639"
[1423] "272643" "276920" "278240" "280287" "280667" "280668"
[1429] "317653" "319177" "319448" "319953" "320022" "320244"
[1435] "320256" "320277" "320558" "320752" "320790" "320878"
[1441] "327826" "328019" "328365" "328401" "328440" "328580"
[1447] "328845" "329557" "329954" "330149" "330188" "330319"
[1453] "330409" "330470" "330830" "330890" "331046" "331416"
[1459] "331537" "332110" "332397" "353188" "353204" "378430"
[1465] "378462" "380654" "380684" "380702" "380709" "380773"
[1471] "380855" "380993" "380994" "381022" "381157" "381196"
[1477] "381218" "381229" "381290" "381404" "381489" "381677"
[1483] "381678" "381759" "382007" "382077" "382113" "382217"
[1489] "382275" "382277" "382301" "383491" "384619" "384806"
[1495] "384813" "387139" "387140" "387153" "387156" "387161"
[1501] "387162" "387177" "387178" "387179" "387188" "387198"
[1507] "387218" "387244" "387245" "387246" "387247" "399599"
[1513] "433700" "434438" "434768" "434784" "434794" "442829"
[1519] "544736" "545156" "546055" "546118" "546272" "546282"
[1525] "574428" "574437" "574438" "619517" "619697" "619991"
[1531] "622480" "622554" "623474" "625249" "625662" "627081"
[1537] "628438" "637277" "664799" "664829" "665270" "665780"
[1543] "666317" "666528" "668110" "668929" "671232" "671564"
[1549] "723849" "723868" "723886" "723932" "723939" "723955"
[1555] "723956" "723962" "723965" "723966" "735262" "735309"
[1561] "751535" "100009600" "100038417" "100038489" "100038977" "100039030"
[1567] "100039065" "100039120" "100039842" "100039905" "100040608" "100040894"
[1573] "100042109" "100042175" "100042922" "100042929" "100042931" "100042939"
[1579] "100042943" "100042944" "100042946" "100043216" "100048534" "100049545"
[1585] "100049546" "100049548" "100113365" "100124460" "100124479" "100124480"
[1591] "100190765" "100270744" "100503361" "100504642" "100861637" "100861881"
[1597] "101055773" "101056116" "101056210" "102443351" "102631559" "102632837"
[1603] "102633564" "102636501" "102638101" "102638793" "102639094" "102639490"
[1609] "102639895" "105247282" "108168511" "108168530" "108168552" "108168557"
[1615] "108168582" "108168594" "113523646" "118451630"
$`GO:0000012`
[1] "11545" "14211" "21958" "22064" "22594" "66408" "70099" "71991"
[9] "72103" "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 8.990006e-05
GO:0019886 20 18 1.0842469 1.303508e-04
GO:1905146 17 17 1.0606304 2.546313e-04
GO:1900424 18 16 1.0750521 2.599783e-04
GO:0002495 24 22 0.9910381 2.629097e-04
GO:0070900 5 5 1.4404406 5.299527e-04
GO:1900864 5 5 1.4404406 5.299527e-04
GO:0002504 26 24 0.9261644 5.672125e-04
GO:0007039 19 19 0.9829004 5.924932e-04
GO:1900426 12 10 1.1666016 5.978555e-04
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:0002495 antigen processing and presentation of peptide antigen via MHC class II
GO:0070900 mitochondrial tRNA modification
GO:1900864 mitochondrial RNA modification
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
GO:0007039 protein catabolic process in the vacuole
GO:1900426 positive regulation of defense response to bacterium
> # 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
52.82 1.67 54.50
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MLP.Rcheck/examples_i386/MLP-Ex.timings
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MLP.Rcheck/examples_x64/MLP-Ex.timings
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