Tobias Verbeke
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/MLP |
| git_branch: RELEASE_3_17 |
| git_last_commit: d9736b7 |
| git_last_commit_date: 2023-04-25 10:18:25 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:15 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 | ||||
| Package 1259/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MLP 1.48.0 (landing page) Tobias Verbeke
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the MLP package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: MLP |
| Version: 1.48.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MLP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MLP_1.48.0.tar.gz |
| StartedAt: 2023-10-16 04:05:15 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 04:21:48 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 992.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MLP.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MLP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MLP_1.48.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/MLP.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MLP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MLP’ version ‘1.48.0’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getGeneSets 120.615 3.427 209.645
addGeneSetDescription 108.872 9.262 155.885
MLP 39.982 1.772 54.548
plot.MLP 6.087 0.133 7.829
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MLP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘MLP’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MLP)
MLP.Rcheck/tests/test.KEGG.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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
83.606 0.667 144.303
>
> 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
92.519 1.226 183.328
MLP.Rcheck/tests/test.MLP.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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, aperm, 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 object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
>
> 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
50.018 5.434 72.709
> goGeneSet[1:3]
$`GO:0000002`
[1] "11545" "12628" "13804" "16882" "17258" "17527" "18975" "19017"
[9] "19819" "20133" "21975" "22059" "23797" "27393" "27395" "27397"
[17] "50776" "57813" "70556" "72170" "72962" "74143" "74244" "74528"
[25] "76781" "83408" "83945" "192287" "216021" "216805" "226153" "230784"
[33] "327762" "381760" "382985" "408022"
$`GO:0000003`
[1] "11287" "11352" "11421" "11430" "11434" "11441"
[7] "11470" "11477" "11479" "11480" "11486" "11495"
[13] "11497" "11498" "11499" "11504" "11516" "11517"
[19] "11545" "11546" "11551" "11552" "11553" "11576"
[25] "11600" "11606" "11614" "11622" "11625" "11643"
[31] "11647" "11651" "11674" "11705" "11747" "11757"
[37] "11774" "11789" "11799" "11804" "11819" "11820"
[43] "11835" "11839" "11857" "11865" "11883" "11920"
[49] "11998" "12009" "12018" "12028" "12034" "12041"
[55] "12043" "12048" "12050" "12053" "12124" "12125"
[61] "12142" "12155" "12159" "12160" "12161" "12162"
[67] "12163" "12164" "12166" "12167" "12168" "12173"
[73] "12190" "12215" "12235" "12236" "12237" "12261"
[79] "12266" "12290" "12305" "12310" "12316" "12317"
[85] "12323" "12363" "12366" "12380" "12387" "12394"
[91] "12411" "12416" "12426" "12427" "12442" "12443"
[97] "12447" "12448" "12458" "12461" "12462" "12464"
[103] "12465" "12466" "12468" "12469" "12505" "12527"
[109] "12530" "12531" "12532" "12550" "12566" "12576"
[115] "12577" "12589" "12593" "12608" "12617" "12638"
[121] "12640" "12659" "12704" "12745" "12753" "12767"
[127] "12801" "12804" "12841" "12846" "12877" "12916"
[133] "12918" "12919" "12929" "12946" "12977" "13006"
[139] "13030" "13039" "13046" "13052" "13070" "13075"
[145] "13121" "13123" "13134" "13164" "13166" "13194"
[151] "13205" "13206" "13214" "13363" "13382" "13383"
[157] "13404" "13411" "13435" "13487" "13488" "13491"
[163] "13492" "13498" "13524" "13525" "13526" "13529"
[169] "13614" "13615" "13617" "13618" "13649" "13653"
[175] "13667" "13711" "13731" "13813" "13831" "13852"
[181] "13854" "13856" "13857" "13866" "13870" "13874"
[187] "13875" "13982" "13983" "14011" "14087" "14088"
[193] "14119" "14155" "14160" "14165" "14178" "14179"
[199] "14180" "14183" "14211" "14228" "14238" "14275"
[205] "14276" "14283" "14308" "14309" "14313" "14347"
[211] "14366" "14367" "14402" "14421" "14425" "14431"
[217] "14447" "14453" "14460" "14462" "14463" "14531"
[223] "14536" "14566" "14595" "14598" "14609" "14610"
[229] "14622" "14626" "14632" "14633" "14654" "14658"
[235] "14682" "14705" "14714" "14725" "14748" "14764"
[241] "14766" "14782" "14810" "14815" "14824" "14841"
[247] "15013" "15018" "15078" "15081" "15110" "15182"
[253] "15194" "15204" "15209" "15211" "15212" "15235"
[259] "15247" "15270" "15361" "15364" "15373" "15375"
[265] "15377" "15378" "15387" "15395" "15396" "15398"
[271] "15405" "15408" "15430" "15431" "15433" "15438"
[277] "15446" "15463" "15482" "15484" "15487" "15488"
[283] "15499" "15500" "15502" "15511" "15512" "15567"
[289] "15574" "15894" "15904" "16000" "16001" "16011"
[295] "16147" "16157" "16158" "16173" "16175" "16176"
[301] "16319" "16322" "16323" "16324" "16330" "16336"
[307] "16337" "16365" "16410" "16412" "16416" "16433"
[313] "16449" "16450" "16477" "16532" "16542" "16578"
[319] "16590" "16601" "16650" "16669" "16691" "16777"
[325] "16783" "16833" "16846" "16847" "16848" "16859"
[331] "16866" "16867" "16869" "16875" "16876" "16878"
[337] "16886" "16952" "16970" "16974" "17125" "17128"
[343] "17129" "17149" "17171" "17173" "17191" "17221"
[349] "17235" "17240" "17242" "17256" "17283" "17289"
[355] "17295" "17300" "17304" "17311" "17345" "17350"
[361] "17381" "17390" "17395" "17427" "17450" "17451"
[367] "17535" "17684" "17685" "17687" "17701" "17702"
[373] "17761" "17771" "17776" "17836" "17864" "17886"
[379] "17977" "17978" "17979" "18000" "18004" "18005"
[385] "18011" "18014" "18072" "18095" "18119" "18121"
[391] "18127" "18128" "18142" "18159" "18168" "18211"
[397] "18285" "18286" "18291" "18292" "18387" "18413"
[403] "18417" "18426" "18429" "18430" "18431" "18436"
[409] "18441" "18442" "18472" "18475" "18476" "18504"
[415] "18507" "18514" "18551" "18552" "18555" "18595"
[421] "18606" "18617" "18663" "18667" "18747" "18749"
[427] "18766" "18775" "18776" "18783" "18787" "18791"
[433] "18792" "18793" "18795" "18802" "18811" "18812"
[439] "18814" "18815" "18817" "18821" "18830" "18858"
[445] "18861" "18952" "19014" "19015" "19049" "19052"
[451] "19057" "19059" "19090" "19109" "19110" "19111"
[457] "19112" "19113" "19114" "19116" "19118" "19119"
[463] "19120" "19143" "19156" "19183" "19204" "19211"
[469] "19214" "19215" "19219" "19223" "19225" "19229"
[475] "19242" "19247" "19275" "19288" "19294" "19317"
[481] "19339" "19353" "19355" "19359" "19360" "19361"
[487] "19362" "19364" "19366" "19401" "19411" "19657"
[493] "19662" "19664" "19701" "19725" "19733" "19735"
[499] "19773" "19821" "19886" "20017" "20104" "20112"
[505] "20181" "20182" "20315" "20317" "20319" "20322"
[511] "20346" "20363" "20377" "20397" "20415" "20423"
[517] "20437" "20473" "20474" "20475" "20520" "20535"
[523] "20613" "20655" "20662" "20670" "20671" "20674"
[529] "20675" "20681" "20682" "20683" "20686" "20687"
[535] "20690" "20708" "20719" "20720" "20724" "20729"
[541] "20730" "20733" "20744" "20758" "20779" "20826"
[547] "20843" "20848" "20850" "20851" "20860" "20869"
[553] "20871" "20873" "20878" "20892" "20897" "20899"
[559] "20905" "20910" "20957" "20962" "20997" "21333"
[565] "21334" "21336" "21337" "21338" "21357" "21386"
[571] "21405" "21410" "21412" "21414" "21416" "21454"
[577] "21463" "21645" "21674" "21679" "21744" "21749"
[583] "21803" "21808" "21812" "21821" "21823" "21824"
[589] "21830" "21833" "21834" "21843" "21849" "21857"
[595] "21869" "21887" "21923" "21930" "21945" "21958"
[601] "21959" "21973" "21974" "22022" "22026" "22059"
[607] "22061" "22064" "22065" "22068" "22092" "22114"
[613] "22115" "22127" "22137" "22174" "22187" "22209"
[619] "22210" "22215" "22223" "22249" "22253" "22334"
[625] "22337" "22339" "22353" "22384" "22412" "22415"
[631] "22417" "22418" "22421" "22431" "22441" "22445"
[637] "22446" "22589" "22632" "22635" "22661" "22668"
[643] "22691" "22694" "22696" "22697" "22698" "22701"
[649] "22702" "22762" "22764" "22768" "22786" "22787"
[655] "22788" "22789" "23793" "23885" "23920" "23950"
[661] "23967" "23968" "23980" "23991" "23997" "24061"
[667] "24084" "24086" "24127" "24128" "26357" "26362"
[673] "26370" "26384" "26407" "26413" "26417" "26423"
[679] "26428" "26434" "26437" "26564" "26565" "26900"
[685] "26909" "26910" "26920" "26927" "26934" "26942"
[691] "26946" "26972" "27061" "27083" "27084" "27206"
[697] "27222" "27354" "27356" "27372" "27386" "28036"
[703] "28078" "28105" "28114" "28135" "29812" "29871"
[709] "29876" "30054" "30841" "30939" "30953" "30959"
[715] "50501" "50505" "50525" "50722" "50790" "50796"
[721] "50878" "50915" "51789" "51792" "51885" "51938"
[727] "52020" "52028" "52679" "52683" "52864" "53381"
[733] "53419" "53422" "53424" "53604" "53614" "53814"
[739] "53857" "53878" "53885" "53897" "53975" "54003"
[745] "54004" "54137" "54140" "54204" "54352" "54383"
[751] "54388" "54418" "54427" "54486" "54524" "54562"
[757] "54608" "54611" "54650" "54725" "55925" "55978"
[763] "55993" "55994" "56092" "56094" "56218" "56220"
[769] "56223" "56228" "56274" "56291" "56296" "56312"
[775] "56334" "56335" "56371" "56436" "56449" "56484"
[781] "56503" "56523" "56526" "56622" "56635" "56693"
[787] "56710" "56711" "56717" "56739" "56746" "57256"
[793] "57264" "57320" "57746" "57749" "57815" "57816"
[799] "57908" "58186" "58226" "58230" "58231" "58864"
[805] "58991" "58998" "59030" "59083" "60530" "60534"
[811] "60597" "60611" "63872" "64009" "64335" "64383"
[817] "64707" "64931" "65247" "65971" "66193" "66197"
[823] "66313" "66392" "66573" "66634" "66654" "66707"
[829] "66712" "66713" "66720" "66722" "66756" "66793"
[835] "66826" "66977" "66983" "67000" "67010" "67027"
[841] "67030" "67031" "67042" "67052" "67077" "67121"
[847] "67141" "67181" "67204" "67231" "67310" "67331"
[853] "67343" "67345" "67374" "67378" "67402" "67504"
[859] "67505" "67555" "67561" "67645" "67652" "67690"
[865] "67713" "67753" "67869" "67909" "67946" "67968"
[871] "67971" "67981" "68107" "68166" "68170" "68231"
[877] "68275" "68298" "68328" "68549" "68708" "68767"
[883] "68911" "68922" "68981" "69032" "69064" "69260"
[889] "69286" "69287" "69306" "69307" "69310" "69329"
[895] "69363" "69376" "69444" "69481" "69538" "69546"
[901] "69707" "69716" "69852" "69865" "69928" "69940"
[907] "69982" "70069" "70093" "70099" "70231" "70235"
[913] "70248" "70375" "70441" "70465" "70503" "70691"
[919] "70772" "70840" "70862" "70873" "70891" "70897"
[925] "70918" "70956" "70977" "71037" "71062" "71078"
[931] "71089" "71099" "71132" "71175" "71233" "71241"
[937] "71242" "71371" "71567" "71709" "71711" "71765"
[943] "71830" "71836" "71840" "71841" "71846" "71860"
[949] "71870" "71904" "71914" "71950" "71981" "72103"
[955] "72135" "72148" "72162" "72236" "72415" "72504"
[961] "72508" "72568" "72634" "72787" "72891" "72938"
[967] "73242" "73244" "73296" "73316" "73329" "73333"
[973] "73336" "73412" "73456" "73463" "73472" "73542"
[979] "73616" "73673" "73677" "73679" "73721" "73862"
[985] "74041" "74052" "74068" "74075" "74090" "74117"
[991] "74174" "74188" "74222" "74229" "74237" "74267"
[997] "74286" "74288" "74297" "74309" "74354" "74360"
[1003] "74362" "74369" "74377" "74383" "74386" "74401"
[1009] "74434" "74446" "74450" "74453" "74468" "74469"
[1015] "74666" "74691" "74708" "74711" "74716" "74717"
[1021] "74754" "74847" "74927" "75002" "75019" "75033"
[1027] "75140" "75178" "75202" "75388" "75410" "75437"
[1033] "75459" "75469" "75514" "75533" "75545" "75571"
[1039] "75596" "75605" "75622" "75641" "75642" "75646"
[1045] "75753" "75773" "75801" "75826" "75828" "75909"
[1051] "76378" "76407" "76421" "76426" "76486" "76499"
[1057] "76573" "76606" "76718" "76800" "76850" "76856"
[1063] "76858" "76867" "76915" "76925" "76943" "77031"
[1069] "77053" "77128" "77254" "77424" "77485" "77505"
[1075] "77595" "77609" "77684" "77772" "77963" "77980"
[1081] "78081" "78118" "78124" "78174" "78284" "78619"
[1087] "78634" "78658" "78784" "78801" "78803" "78925"
[1093] "80297" "80517" "80838" "80884" "80912" "81018"
[1099] "81601" "83434" "83456" "83557" "83558" "83560"
[1105] "83561" "83964" "83984" "93670" "93684" "93730"
[1111] "93736" "93757" "93759" "93760" "93837" "93960"
[1117] "94109" "94221" "94224" "94244" "94246" "97086"
[1123] "97165" "98558" "98711" "99412" "99929" "100121"
[1129] "100155" "100317" "100535" "100986" "101100" "101187"
[1135] "101476" "102774" "102991" "103468" "103554" "103583"
[1141] "103733" "103768" "104111" "104156" "104263" "104271"
[1147] "104346" "104362" "104601" "104799" "104806" "105349"
[1153] "105511" "105988" "106389" "106757" "107515" "107626"
[1159] "107656" "107849" "107970" "107995" "108829" "108961"
[1165] "109685" "109689" "109785" "110012" "110082" "110084"
[1171] "110147" "110355" "110542" "110957" "110958" "112418"
[1177] "114602" "114606" "114642" "114661" "114662" "114714"
[1183] "114875" "116837" "116914" "140498" "140557" "170731"
[1189] "171285" "171429" "171506" "192119" "192176" "192195"
[1195] "192199" "192236" "192897" "193322" "193838" "194908"
[1201] "195434" "207304" "207352" "207607" "207686" "208144"
[1207] "208169" "208188" "208727" "208908" "209011" "209091"
[1213] "210510" "210529" "210554" "211484" "211651" "212517"
[1219] "212670" "212937" "213081" "213236" "213272" "213389"
[1225] "213402" "213541" "213742" "214105" "214290" "214321"
[1231] "214384" "214575" "214593" "214901" "215028" "215029"
[1237] "215095" "215387" "215772" "215854" "216350" "216725"
[1243] "216869" "217039" "217116" "217216" "217341" "217715"
[1249] "217716" "218214" "218454" "219038" "223593" "223697"
[1255] "223825" "223921" "223989" "224045" "224171" "224661"
[1261] "224727" "224826" "224902" "225182" "225497" "225865"
[1267] "225922" "226049" "226090" "226162" "226265" "226356"
[1273] "227210" "227394" "227615" "227631" "227707" "227736"
[1279] "228421" "228980" "229096" "229227" "229357" "229841"
[1285] "229906" "230103" "230126" "230594" "230700" "230861"
[1291] "230899" "231051" "231386" "231600" "231633" "231832"
[1297] "231912" "232174" "232223" "232286" "232345" "232664"
[1303] "232816" "232943" "233276" "234396" "234857" "235072"
[1309] "235320" "235330" "235345" "235380" "235559" "235628"
[1315] "236266" "236899" "237336" "237625" "237911" "237958"
[1321] "238055" "238057" "238217" "238247" "238330" "238405"
[1327] "238406" "239083" "239528" "239591" "239731" "240023"
[1333] "240069" "240255" "240590" "240697" "240725" "240899"
[1339] "241116" "241296" "241516" "241624" "242202" "242523"
[1345] "242620" "243862" "243866" "243897" "244199" "244486"
[1351] "244495" "244551" "244891" "245000" "245865" "245884"
[1357] "245944" "246747" "252828" "252866" "252868" "252967"
[1363] "252973" "258658" "259279" "260305" "263876" "264134"
[1369] "268396" "268420" "268465" "268491" "268591" "268697"
[1375] "268755" "268860" "268903" "269254" "269275" "269610"
[1381] "269682" "269701" "270624" "271036" "271127" "271564"
[1387] "271639" "272643" "276920" "278203" "278240" "280287"
[1393] "280667" "280668" "317653" "317755" "319177" "319448"
[1399] "319953" "320022" "320214" "320244" "320256" "320277"
[1405] "320406" "320558" "320752" "320790" "320869" "327826"
[1411] "328019" "328365" "328401" "328440" "328580" "328845"
[1417] "329557" "329702" "329954" "330149" "330188" "330277"
[1423] "330319" "330409" "330470" "330830" "330890" "331046"
[1429] "331416" "331491" "331537" "332110" "332397" "333307"
[1435] "333564" "353188" "353320" "353342" "378430" "378462"
[1441] "380654" "380684" "380702" "380709" "380773" "380855"
[1447] "380994" "381022" "381157" "381196" "381218" "381229"
[1453] "381290" "381350" "381404" "381489" "381598" "381677"
[1459] "381678" "381759" "382007" "382077" "382113" "382217"
[1465] "382275" "382277" "382301" "382562" "383491" "384619"
[1471] "384806" "384813" "387139" "387140" "387153" "387156"
[1477] "387161" "387162" "387177" "387178" "387179" "387188"
[1483] "387198" "387218" "387244" "387245" "387246" "387247"
[1489] "399599" "433700" "434438" "434555" "434768" "434784"
[1495] "434794" "442829" "544752" "545156" "545391" "545824"
[1501] "546055" "546118" "546272" "546282" "546886" "574428"
[1507] "574437" "574438" "619517" "619697" "619991" "622480"
[1513] "622554" "623131" "623474" "625249" "625662" "627081"
[1519] "628438" "631584" "636104" "637277" "664829" "665270"
[1525] "665780" "666173" "666317" "666528" "668110" "668929"
[1531] "671232" "671564" "723849" "723868" "723886" "723932"
[1537] "723939" "723955" "723956" "723962" "723965" "723966"
[1543] "735262" "735309" "751535" "100009600" "100038417" "100038489"
[1549] "100038977" "100039030" "100039065" "100039120" "100039842" "100039905"
[1555] "100040608" "100040894" "100042109" "100042175" "100042922" "100042929"
[1561] "100042931" "100042939" "100042943" "100042944" "100042946" "100043216"
[1567] "100048534" "100049545" "100049546" "100049548" "100113365" "100124460"
[1573] "100124479" "100124480" "100190765" "100270744" "100503361" "100504207"
[1579] "100504642" "100861637" "100861881" "101055773" "101056116" "101056210"
[1585] "102631559" "102632837" "102633564" "102636501" "102638101" "102638793"
[1591] "102639094" "102639490" "102639895" "105243794" "105247282" "108168511"
[1597] "108168530" "108168552" "108168557" "108168582" "108168594" "113523646"
[1603] "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:0019886 21 18 1.0842469 0.0001162057
GO:0002495 25 22 0.9910381 0.0002373259
GO:0002504 27 24 0.9261644 0.0005627878
GO:1905146 19 19 0.9741769 0.0006361075
GO:0002478 29 26 0.8824480 0.0009481949
GO:0007039 21 21 0.9120835 0.0012384292
GO:0048524 69 60 0.7013955 0.0014377541
GO:1900424 22 20 0.9063168 0.0016220339
GO:0010813 5 5 1.3587164 0.0016343746
GO:0019884 36 31 0.8074586 0.0019627554
geneSetDescription
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0002495 antigen processing and presentation of peptide antigen via MHC class II
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
GO:1905146 lysosomal protein catabolic process
GO:0002478 antigen processing and presentation of exogenous peptide antigen
GO:0007039 protein catabolic process in the vacuole
GO:0048524 positive regulation of viral process
GO:1900424 regulation of defense response to bacterium
GO:0010813 neuropeptide catabolic process
GO:0019884 antigen processing and presentation of exogenous antigen
> # 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
95.941 9.161 139.676
MLP.Rcheck/MLP-Ex.timings
| name | user | system | elapsed | |
| MLP | 39.982 | 1.772 | 54.548 | |
| addGeneSetDescription | 108.872 | 9.262 | 155.885 | |
| getGeneSets | 120.615 | 3.427 | 209.645 | |
| mlpBarplot | 0.031 | 0.004 | 0.036 | |
| plot.MLP | 6.087 | 0.133 | 7.829 | |
| plotGOgraph | 1.170 | 0.025 | 1.512 | |
| plotGeneSetSignificance | 1.232 | 0.052 | 1.672 | |