Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:12 -0400 (Fri, 15 Oct 2021).
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1163/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MLP 1.40.0 (landing page) Tobias Verbeke
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.40.0 |
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 |
############################################################################## ############################################################################## ### ### 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
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
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 |
MLP.Rcheck/examples_i386/MLP-Ex.timings
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MLP.Rcheck/examples_x64/MLP-Ex.timings
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