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MLP.Rcheck/tests_i386/test.MLP.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
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> require(MLP)
Loading required package: MLP
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, 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, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: affy
Loading required package: plotrix
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:plotrix':
plotCI
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Loading required package: gmodels
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: 'gdata'
The following object is masked from 'package:gplots':
reorder.factor
The following object is masked from 'package:IRanges':
trim
The following objects are masked from 'package:S4Vectors':
first, first<-
The following object is masked from 'package:Biobase':
combine
The following object is masked from 'package:BiocGenerics':
combine
The following object is masked from 'package:stats4':
nobs
The following object is masked from 'package:stats':
nobs
The following object is masked from 'package:utils':
object.size
The following object is masked from 'package:base':
startsWith
Loading required package: gtools
> set.seed(479)
>
> # This is just the expressionset for this experiment.
>
> pathExampleData <- system.file("exampleFiles", "expressionSetGcrma.rda", package = "MLP")
> load(pathExampleData)
>
> # Libraries needed
> library(limma)
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
> library(org.Mm.eg.db) # for mouse
>
> exprs(expressionSetGcrma)[1:2,]
2760 2763 2765 2766 2768 2769 2761
100009600 2.371111 2.170060 2.233383 2.180717 2.325886 2.239441 2.297301
100012 2.176163 2.318876 2.419263 2.223307 2.585125 2.346060 2.292061
2762 2764 2767 2770 2771
100009600 2.409001 2.49458 2.115814 2.371262 2.267459
100012 2.336415 2.47979 2.361981 2.330418 2.520918
> # 2760 2763 2765 2766 2768 2769 2761 2762 2764 2767
> #100009600 2.371111 2.170060 2.233383 2.180717 2.325886 2.239441 2.297301 2.409001 2.49458 2.115814
> #100012 2.176163 2.318876 2.419263 2.223307 2.585125 2.346060 2.292061 2.336415 2.47979 2.361981
> # 2770 2771
> #100009600 2.371262 2.267459
> #100012 2.330418 2.520918
>
> pData(expressionSetGcrma)
sample subGroup sampleColor subGroup1
2760 1 1 #FF0000 WT
2763 4 1 #FF0000 WT
2765 6 1 #FF0000 WT
2766 7 1 #FF0000 WT
2768 9 1 #FF0000 WT
2769 10 1 #FF0000 WT
2761 2 2 #0000FF KO
2762 3 2 #0000FF KO
2764 5 2 #0000FF KO
2767 8 2 #0000FF KO
2770 11 2 #0000FF KO
2771 12 2 #0000FF KO
> # sample subGroup sampleColor
> #2760 1 1 #FF0000
> #2763 4 1 #FF0000
> #2765 6 1 #FF0000
> #2766 7 1 #FF0000
> #2768 9 1 #FF0000
> #2769 10 1 #FF0000
> #2761 2 2 #0000FF
> #2762 3 2 #0000FF
> #2764 5 2 #0000FF
> #2767 8 2 #0000FF
> #2770 11 2 #0000FF
> #2771 12 2 #0000FF
>
> pData(expressionSetGcrma)$subGroup1 <- ifelse(pData(expressionSetGcrma)$subGroup==1,"WT","KO")
>
> ###==============================================GENERATING LIMMA p-VALUES=================================
>
> # boxplot(data.frame(exprs(expressionSetGcrma))
> normDat <- normalizeQuantiles(exprs(expressionSetGcrma), ties=TRUE)
> subGroup <- pData(expressionSetGcrma)$subGroup
> design <- model.matrix(~ -1 +factor(subGroup ))
>
> colnames(design) <- c("group1", "group2")
> contrast.matrix <- makeContrasts(group1-group2, levels=design)
> fit <- lmFit(normDat,design)
> fit2 <- contrasts.fit(fit, contrast.matrix)
> fit2 <- eBayes(fit2)
> normDat.p <- fit2$p.value
>
> normDat.p[1:5]
[1] 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761
> #[1] 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761
>
> system.time(goGeneSet <- getGeneSets(species = "Mouse", geneSetSource = "GOBP", entrezIdentifiers = featureNames(expressionSetGcrma)))
Loading required package: GO.db
user system elapsed
31.75 5.80 37.55
> goGeneSet[1:3]
$`GO:0000002`
[1] "11545" "16882" "17258" "17527" "19017" "21975" "22059" "23797"
[9] "27393" "27395" "27397" "50776" "57813" "70556" "72170" "72962"
[17] "74143" "74528" "83408" "192287" "216021" "216805" "229524" "230784"
[25] "327762"
$`GO:0000003`
[1] "11287" "11352" "11421" "11430" "11434" "11441"
[7] "11477" "11479" "11480" "11486" "11495" "11497"
[13] "11504" "11516" "11517" "11535" "11551" "11552"
[19] "11553" "11576" "11600" "11606" "11614" "11622"
[25] "11625" "11643" "11647" "11651" "11674" "11705"
[31] "11747" "11757" "11789" "11797" "11804" "11819"
[37] "11820" "11835" "11839" "11857" "11863" "11865"
[43] "11883" "11920" "11998" "12009" "12018" "12028"
[49] "12034" "12043" "12048" "12050" "12053" "12124"
[55] "12125" "12142" "12155" "12159" "12160" "12161"
[61] "12162" "12163" "12164" "12166" "12167" "12168"
[67] "12173" "12190" "12192" "12211" "12235" "12236"
[73] "12237" "12261" "12290" "12305" "12310" "12316"
[79] "12317" "12323" "12344" "12363" "12366" "12380"
[85] "12387" "12394" "12411" "12416" "12426" "12427"
[91] "12443" "12447" "12448" "12449" "12458" "12461"
[97] "12462" "12464" "12465" "12466" "12468" "12469"
[103] "12505" "12527" "12530" "12531" "12532" "12550"
[109] "12566" "12576" "12577" "12589" "12591" "12592"
[115] "12593" "12606" "12608" "12617" "12638" "12640"
[121] "12659" "12702" "12704" "12705" "12745" "12753"
[127] "12767" "12801" "12804" "12841" "12846" "12877"
[133] "12916" "12918" "12919" "12929" "12946" "12977"
[139] "12981" "13006" "13030" "13039" "13046" "13052"
[145] "13070" "13075" "13123" "13134" "13164" "13166"
[151] "13205" "13206" "13363" "13382" "13383" "13393"
[157] "13404" "13411" "13435" "13487" "13488" "13491"
[163] "13492" "13498" "13524" "13525" "13526" "13529"
[169] "13615" "13617" "13618" "13649" "13653" "13667"
[175] "13731" "13813" "13819" "13852" "13854" "13856"
[181] "13857" "13866" "13870" "13874" "13875" "13982"
[187] "13983" "13984" "14008" "14011" "14087" "14088"
[193] "14155" "14160" "14165" "14178" "14179" "14180"
[199] "14183" "14211" "14228" "14238" "14276" "14283"
[205] "14308" "14309" "14313" "14366" "14367" "14388"
[211] "14421" "14431" "14447" "14453" "14460" "14461"
[217] "14462" "14463" "14531" "14536" "14566" "14595"
[223] "14598" "14609" "14610" "14620" "14622" "14632"
[229] "14633" "14654" "14658" "14682" "14705" "14714"
[235] "14725" "14748" "14764" "14766" "14782" "14784"
[241] "14810" "14815" "14824" "15013" "15018" "15078"
[247] "15081" "15110" "15182" "15194" "15204" "15205"
[253] "15211" "15212" "15213" "15214" "15221" "15235"
[259] "15247" "15251" "15270" "15361" "15364" "15373"
[265] "15375" "15377" "15378" "15387" "15395" "15396"
[271] "15398" "15405" "15408" "15423" "15430" "15431"
[277] "15433" "15438" "15446" "15463" "15482" "15484"
[283] "15486" "15487" "15488" "15499" "15500" "15502"
[289] "15511" "15512" "15516" "15567" "15570" "15574"
[295] "15894" "15904" "16000" "16001" "16002" "16007"
[301] "16011" "16147" "16153" "16157" "16173" "16175"
[307] "16176" "16322" "16323" "16324" "16330" "16336"
[313] "16337" "16365" "16401" "16410" "16412" "16433"
[319] "16450" "16477" "16532" "16542" "16590" "16601"
[325] "16650" "16669" "16691" "16777" "16783" "16833"
[331] "16842" "16846" "16847" "16848" "16859" "16866"
[337] "16867" "16869" "16871" "16872" "16875" "16876"
[343] "16878" "16886" "16952" "16970" "16974" "17125"
[349] "17128" "17129" "17149" "17171" "17173" "17191"
[355] "17221" "17235" "17240" "17242" "17256" "17283"
[361] "17289" "17295" "17300" "17304" "17311" "17319"
[367] "17345" "17350" "17381" "17390" "17395" "17427"
[373] "17450" "17451" "17535" "17684" "17685" "17686"
[379] "17687" "17688" "17701" "17702" "17761" "17771"
[385] "17776" "17836" "17864" "17886" "17977" "17978"
[391] "17979" "17986" "18000" "18004" "18005" "18011"
[397] "18014" "18022" "18072" "18095" "18119" "18121"
[403] "18127" "18128" "18129" "18142" "18159" "18168"
[409] "18194" "18211" "18285" "18286" "18291" "18292"
[415] "18387" "18413" "18417" "18426" "18429" "18430"
[421] "18431" "18436" "18441" "18442" "18472" "18475"
[427] "18476" "18504" "18507" "18514" "18551" "18552"
[433] "18555" "18591" "18595" "18606" "18617" "18663"
[439] "18667" "18671" "18747" "18749" "18763" "18764"
[445] "18766" "18775" "18776" "18783" "18787" "18791"
[451] "18792" "18793" "18795" "18799" "18802" "18811"
[457] "18812" "18814" "18815" "18817" "18830" "18858"
[463] "18861" "18952" "19014" "19015" "19016" "19049"
[469] "19052" "19059" "19090" "19109" "19110" "19111"
[475] "19112" "19113" "19114" "19116" "19118" "19119"
[481] "19120" "19143" "19156" "19183" "19204" "19211"
[487] "19214" "19215" "19219" "19223" "19225" "19229"
[493] "19242" "19247" "19275" "19288" "19294" "19317"
[499] "19339" "19355" "19357" "19359" "19360" "19361"
[505] "19366" "19401" "19411" "19662" "19664" "19701"
[511] "19725" "19733" "19735" "19773" "19821" "19886"
[517] "20017" "20104" "20112" "20181" "20182" "20315"
[523] "20317" "20319" "20322" "20346" "20363" "20377"
[529] "20397" "20415" "20423" "20437" "20474" "20475"
[535] "20520" "20541" "20613" "20655" "20662" "20671"
[541] "20674" "20675" "20681" "20682" "20683" "20686"
[547] "20687" "20690" "20708" "20719" "20720" "20724"
[553] "20729" "20730" "20732" "20733" "20744" "20758"
[559] "20779" "20826" "20843" "20848" "20850" "20851"
[565] "20860" "20869" "20871" "20873" "20878" "20892"
[571] "20897" "20899" "20905" "20910" "20957" "20962"
[577] "20997" "21336" "21337" "21338" "21357" "21386"
[583] "21405" "21410" "21412" "21414" "21416" "21425"
[589] "21454" "21463" "21645" "21674" "21679" "21744"
[595] "21749" "21803" "21808" "21812" "21821" "21823"
[601] "21824" "21830" "21833" "21834" "21843" "21849"
[607] "21857" "21869" "21887" "21923" "21945" "21958"
[613] "21959" "21973" "21974" "22022" "22026" "22061"
[619] "22064" "22065" "22068" "22092" "22113" "22114"
[625] "22115" "22127" "22137" "22174" "22187" "22209"
[631] "22210" "22215" "22249" "22329" "22334" "22337"
[637] "22339" "22353" "22371" "22384" "22412" "22413"
[643] "22415" "22417" "22418" "22421" "22422" "22431"
[649] "22441" "22445" "22446" "22589" "22632" "22635"
[655] "22661" "22668" "22691" "22694" "22696" "22697"
[661] "22698" "22701" "22702" "22762" "22764" "22768"
[667] "22786" "22787" "22788" "22789" "23793" "23885"
[673] "23920" "23950" "23967" "23968" "23980" "23991"
[679] "23997" "24061" "24084" "24086" "24127" "24128"
[685] "26357" "26362" "26366" "26370" "26380" "26384"
[691] "26395" "26407" "26413" "26416" "26417" "26423"
[697] "26434" "26437" "26564" "26900" "26909" "26910"
[703] "26927" "26934" "26942" "26946" "26972" "27061"
[709] "27083" "27084" "27206" "27222" "27354" "27356"
[715] "27372" "27386" "28036" "28078" "28088" "28105"
[721] "28114" "28135" "29871" "29876" "30054" "30841"
[727] "30939" "30953" "30959" "50500" "50501" "50505"
[733] "50525" "50722" "50785" "50790" "50796" "50878"
[739] "50915" "51789" "51792" "51885" "51938" "52020"
[745] "52028" "52679" "52683" "52864" "53381" "53419"
[751] "53422" "53424" "53601" "53604" "53614" "53814"
[757] "53878" "53885" "53897" "53975" "54003" "54004"
[763] "54137" "54140" "54204" "54383" "54388" "54418"
[769] "54427" "54486" "54524" "54562" "54608" "54611"
[775] "54650" "54725" "55925" "55978" "55993" "55994"
[781] "56092" "56094" "56096" "56213" "56218" "56220"
[787] "56223" "56228" "56274" "56291" "56312" "56334"
[793] "56335" "56371" "56406" "56436" "56449" "56484"
[799] "56503" "56523" "56526" "56635" "56693" "56710"
[805] "56711" "56717" "56739" "56746" "57256" "57264"
[811] "57320" "57746" "57749" "57815" "57816" "57908"
[817] "58186" "58226" "58230" "58231" "58864" "58991"
[823] "58998" "59030" "59083" "60530" "60534" "60597"
[829] "63872" "64009" "64335" "64383" "64707" "64931"
[835] "65247" "65971" "66197" "66313" "66392" "66404"
[841] "66515" "66573" "66634" "66654" "66707" "66712"
[847] "66713" "66720" "66722" "66793" "66923" "66977"
[853] "66983" "67000" "67010" "67030" "67042" "67077"
[859] "67121" "67141" "67181" "67204" "67231" "67310"
[865] "67331" "67333" "67345" "67378" "67402" "67504"
[871] "67505" "67555" "67561" "67652" "67690" "67713"
[877] "67753" "67869" "67909" "67946" "67968" "67981"
[883] "68107" "68166" "68170" "68231" "68265" "68275"
[889] "68298" "68328" "68549" "68708" "68767" "68911"
[895] "68922" "68981" "69032" "69064" "69260" "69286"
[901] "69287" "69306" "69307" "69310" "69376" "69444"
[907] "69538" "69546" "69707" "69716" "69852" "69865"
[913] "69928" "69982" "70069" "70093" "70099" "70231"
[919] "70235" "70248" "70375" "70441" "70465" "70503"
[925] "70691" "70772" "70840" "70862" "70873" "70891"
[931] "70918" "70956" "70977" "71062" "71089" "71099"
[937] "71132" "71175" "71241" "71242" "71371" "71567"
[943] "71709" "71711" "71765" "71830" "71836" "71840"
[949] "71846" "71854" "71904" "71914" "71950" "71981"
[955] "72135" "72148" "72162" "72236" "72415" "72469"
[961] "72504" "72508" "72568" "72634" "72780" "72787"
[967] "72891" "72938" "73242" "73244" "73296" "73316"
[973] "73329" "73336" "73412" "73456" "73472" "73542"
[979] "73616" "73673" "73679" "73721" "74041" "74068"
[985] "74075" "74090" "74117" "74174" "74188" "74229"
[991] "74237" "74267" "74286" "74288" "74297" "74309"
[997] "74354" "74360" "74369" "74386" "74401" "74434"
[1003] "74446" "74450" "74468" "74469" "74691" "74708"
[1009] "74716" "74754" "74847" "74927" "75019" "75033"
[1015] "75140" "75178" "75202" "75388" "75410" "75459"
[1021] "75469" "75514" "75533" "75571" "75596" "75605"
[1027] "75622" "75642" "75646" "75753" "75801" "75826"
[1033] "75828" "75909" "76378" "76407" "76486" "76499"
[1039] "76718" "76800" "76850" "76856" "76858" "76867"
[1045] "76915" "76925" "76943" "77053" "77128" "77424"
[1051] "77595" "77684" "77963" "77980" "78081" "78124"
[1057] "78284" "78619" "78634" "78658" "78784" "78801"
[1063] "78803" "78925" "80297" "80517" "80838" "80884"
[1069] "80912" "81018" "83456" "83557" "83558" "83560"
[1075] "83561" "83964" "83984" "93684" "93736" "93757"
[1081] "93759" "93760" "93837" "93960" "94221" "94224"
[1087] "94244" "94246" "97086" "97165" "98558" "98711"
[1093] "99412" "99929" "100121" "100155" "100317" "100535"
[1099] "100986" "101187" "101476" "102774" "103468" "103554"
[1105] "103733" "103768" "104083" "104111" "104148" "104156"
[1111] "104263" "104271" "104310" "104346" "104362" "104601"
[1117] "104799" "104806" "105349" "105511" "105988" "106389"
[1123] "106757" "107515" "107586" "107626" "107656" "107849"
[1129] "107970" "107995" "108829" "108961" "109685" "109689"
[1135] "109727" "109785" "110012" "110082" "110084" "110147"
[1141] "110355" "110459" "110542" "110957" "110958" "112405"
[1147] "114606" "114642" "114661" "114662" "114714" "114875"
[1153] "116837" "140498" "140557" "170676" "171285" "171429"
[1159] "171506" "191578" "192119" "192176" "192195" "192199"
[1165] "192897" "193838" "194908" "195434" "207165" "207304"
[1171] "207352" "207607" "207686" "208169" "208188" "208727"
[1177] "209091" "209351" "210510" "210529" "210554" "211064"
[1183] "211484" "211651" "212517" "212670" "212937" "213081"
[1189] "213236" "213272" "213389" "213541" "213742" "214105"
[1195] "214253" "214290" "214292" "214384" "214572" "214575"
[1201] "214593" "214901" "215028" "215029" "215095" "215387"
[1207] "215854" "216350" "216725" "216869" "217039" "217116"
[1213] "217325" "217715" "217716" "218214" "218454" "218914"
[1219] "223593" "223697" "223825" "223921" "223989" "224045"
[1225] "224171" "224661" "224727" "224826" "224902" "225182"
[1231] "225865" "226090" "226162" "226265" "226841" "227210"
[1237] "227394" "227615" "227631" "227736" "228421" "228980"
[1243] "229227" "229357" "229700" "230103" "230126" "230594"
[1249] "230809" "230861" "230899" "231051" "231386" "231633"
[1255] "231672" "231832" "231912" "232174" "232223" "232286"
[1261] "232345" "232664" "233276" "233328" "234857" "235072"
[1267] "235320" "235559" "235626" "235628" "236266" "236899"
[1273] "237336" "237625" "237911" "238055" "238057" "238247"
[1279] "238328" "238330" "239083" "239167" "239528" "239731"
[1285] "240069" "240255" "240590" "240697" "240725" "240899"
[1291] "241624" "242202" "242523" "243862" "243897" "243905"
[1297] "244551" "245000" "245865" "246747" "252828" "252868"
[1303] "252967" "252973" "259279" "260305" "264134" "268396"
[1309] "268420" "268465" "268491" "268591" "268697" "268755"
[1315] "268860" "268903" "268930" "269254" "269275" "269610"
[1321] "269682" "269701" "270624" "271036" "271127" "271639"
[1327] "272643" "276920" "277353" "278240" "280287" "280667"
[1333] "280668" "317653" "319177" "319448" "319953" "320022"
[1339] "320244" "320277" "320558" "320752" "320790" "327826"
[1345] "328019" "328365" "328401" "328440" "328580" "328845"
[1351] "329557" "329954" "330149" "330188" "330319" "330409"
[1357] "330470" "330830" "330890" "331046" "331416" "332110"
[1363] "378430" "378462" "380654" "380684" "380702" "380709"
[1369] "380773" "380855" "380993" "380994" "381022" "381157"
[1375] "381196" "381290" "381404" "381489" "381677" "381759"
[1381] "382077" "382217" "382275" "382277" "382301" "383491"
[1387] "384619" "387139" "387140" "387153" "387156" "387161"
[1393] "387162" "387177" "387178" "387179" "387188" "387198"
[1399] "387218" "387244" "387245" "387246" "387247" "399599"
[1405] "433700" "434438" "434784" "434794" "442829" "545156"
[1411] "546118" "546272" "546282" "574428" "574437" "574438"
[1417] "619517" "619697" "619991" "622554" "623474" "625249"
[1423] "625662" "627081" "629389" "664799" "664829" "665187"
[1429] "665270" "665780" "666317" "666528" "668110" "668929"
[1435] "671232" "671564" "723849" "723868" "723886" "723932"
[1441] "723939" "723955" "723956" "723962" "723965" "723966"
[1447] "735262" "735309" "751535" "100009600" "100038417" "100038489"
[1453] "100038977" "100039030" "100039065" "100039120" "100039842" "100039905"
[1459] "100040483" "100040608" "100040894" "100042109" "100042175" "100042922"
[1465] "100042929" "100042931" "100042939" "100042943" "100042944" "100042946"
[1471] "100043216" "100048534" "100049545" "100049546" "100049548" "100113365"
[1477] "100124460" "100124479" "100124480" "100190765" "100270744" "100504642"
[1483] "100861637" "100861881" "101055773" "101056116" "101056210" "102443351"
[1489] "102631559" "102632183" "102633564" "102636501" "102638101" "102638793"
[1495] "102639094" "102639490" "102639895" "105247282" "108168552" "108168557"
[1501] "108168582" "108168594" "113523646"
$`GO:0000012`
[1] "11545" "14211" "22064" "22594" "66408" "70099" "72103" "93759"
[9] "104884" "319583"
> # output changes with annotation version !
>
> y <- normDat.p[,1]
> names(y) <- featureNames(expressionSetGcrma)
>
> y[1:10]
100009600 100012 100017 100019 100034251 100036521 100037258 100037278
0.4328583 0.7448996 0.6088859 0.1845008 0.2312761 0.7865153 0.7772888 0.1037431
100038570 100038635
0.1368744 0.3272610
> # 100009600 100012 100017 100019 100034251 100036521 100037258 100037278
> # 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761 0.7865153 0.7772888 0.1037431
> # 100038570 100038635
> # 0.1368744 0.3272610
>
> mlpObject <- MLP(geneSet = goGeneSet, geneStatistic = y, minGenes = 5, maxGenes = 100, rowPermutations = TRUE,
+ nPermutations = 6, smoothPValues = TRUE)
>
>
>
> mlpObject[1:10, ]
totalGeneSetSize testedGeneSetSize geneSetStatistic geneSetPValue
GO:0002282 5 5 1.6379883 0.0001425143
GO:1900426 12 10 1.1666016 0.0003970342
GO:0019886 14 14 1.0549211 0.0004675798
GO:0060179 12 10 1.1332820 0.0006140852
GO:1900424 19 17 0.9799674 0.0007850341
GO:0002468 11 9 1.1429532 0.0008683572
GO:0002495 19 19 0.9388391 0.0010271824
GO:0002478 25 24 0.8798107 0.0010911776
GO:1903334 6 5 1.3744357 0.0012863305
GO:0002504 20 20 0.9113723 0.0013290942
geneSetDescription
GO:0002282 microglial cell activation involved in immune response
GO:1900426 positive regulation of defense response to bacterium
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0060179 male mating behavior
GO:1900424 regulation of defense response to bacterium
GO:0002468 dendritic cell antigen processing and presentation
GO:0002495 antigen processing and presentation of peptide antigen via MHC class II
GO:0002478 antigen processing and presentation of exogenous peptide antigen
GO:1903334 positive regulation of protein folding
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
> # output changes with annotation version !
>
> plotGOgraph(object = mlpObject, main = "test of main")
Loading required package: Rgraphviz
Loading required package: graph
Loading required package: grid
Attaching package: 'Rgraphviz'
The following objects are masked from 'package:IRanges':
from, to
The following objects are masked from 'package:S4Vectors':
from, to
Loading required package: GOstats
Loading required package: Category
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Attaching package: 'GOstats'
The following object is masked from 'package:AnnotationDbi':
makeGOGraph
Loading required package: annotate
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
Attaching package: 'annotate'
The following object is masked from 'package:Rgraphviz':
toFile
>
> pdf(file = "test10.pdf", width = 10, height = 10)
> # x11(width = 10, height = 10)
> plot(mlpObject, nRow = 10) # by default: type = "barplot"
> dev.off()
pdf
2
>
> unlink("test10.pdf")
>
> if (FALSE){
+ pdf(file = "test5.pdf", width =10, height = 10)
+ mlpBarplot(object = mlpObject, geneSetSource = "GOBP", nRow = 10, descriptionLength = 5)
+ dev.off()
+
+ unlink("test5.pdf")
+
+ pdf(file = "test100.pdf", width =10, height = 20)
+ mlpBarplot(object = mlpObject, geneSetSource = "GOBP", nRow = 10, descriptionLength = 100)
+ dev.off()
+
+ unlink("test100.pdf")
+ }
>
> plot(mlpObject, type = "quantileCurves")
> plot(mlpObject, type = "GOgraph")
>
> proc.time()
user system elapsed
55.29 6.26 62.85
|
MLP.Rcheck/tests_x64/test.MLP.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require(MLP)
Loading required package: MLP
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, 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, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: affy
Loading required package: plotrix
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:plotrix':
plotCI
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Loading required package: gmodels
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: 'gdata'
The following object is masked from 'package:gplots':
reorder.factor
The following object is masked from 'package:IRanges':
trim
The following objects are masked from 'package:S4Vectors':
first, first<-
The following object is masked from 'package:Biobase':
combine
The following object is masked from 'package:BiocGenerics':
combine
The following object is masked from 'package:stats4':
nobs
The following object is masked from 'package:stats':
nobs
The following object is masked from 'package:utils':
object.size
The following object is masked from 'package:base':
startsWith
Loading required package: gtools
> set.seed(479)
>
> # This is just the expressionset for this experiment.
>
> pathExampleData <- system.file("exampleFiles", "expressionSetGcrma.rda", package = "MLP")
> load(pathExampleData)
>
> # Libraries needed
> library(limma)
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
> library(org.Mm.eg.db) # for mouse
>
> exprs(expressionSetGcrma)[1:2,]
2760 2763 2765 2766 2768 2769 2761
100009600 2.371111 2.170060 2.233383 2.180717 2.325886 2.239441 2.297301
100012 2.176163 2.318876 2.419263 2.223307 2.585125 2.346060 2.292061
2762 2764 2767 2770 2771
100009600 2.409001 2.49458 2.115814 2.371262 2.267459
100012 2.336415 2.47979 2.361981 2.330418 2.520918
> # 2760 2763 2765 2766 2768 2769 2761 2762 2764 2767
> #100009600 2.371111 2.170060 2.233383 2.180717 2.325886 2.239441 2.297301 2.409001 2.49458 2.115814
> #100012 2.176163 2.318876 2.419263 2.223307 2.585125 2.346060 2.292061 2.336415 2.47979 2.361981
> # 2770 2771
> #100009600 2.371262 2.267459
> #100012 2.330418 2.520918
>
> pData(expressionSetGcrma)
sample subGroup sampleColor subGroup1
2760 1 1 #FF0000 WT
2763 4 1 #FF0000 WT
2765 6 1 #FF0000 WT
2766 7 1 #FF0000 WT
2768 9 1 #FF0000 WT
2769 10 1 #FF0000 WT
2761 2 2 #0000FF KO
2762 3 2 #0000FF KO
2764 5 2 #0000FF KO
2767 8 2 #0000FF KO
2770 11 2 #0000FF KO
2771 12 2 #0000FF KO
> # sample subGroup sampleColor
> #2760 1 1 #FF0000
> #2763 4 1 #FF0000
> #2765 6 1 #FF0000
> #2766 7 1 #FF0000
> #2768 9 1 #FF0000
> #2769 10 1 #FF0000
> #2761 2 2 #0000FF
> #2762 3 2 #0000FF
> #2764 5 2 #0000FF
> #2767 8 2 #0000FF
> #2770 11 2 #0000FF
> #2771 12 2 #0000FF
>
> pData(expressionSetGcrma)$subGroup1 <- ifelse(pData(expressionSetGcrma)$subGroup==1,"WT","KO")
>
> ###==============================================GENERATING LIMMA p-VALUES=================================
>
> # boxplot(data.frame(exprs(expressionSetGcrma))
> normDat <- normalizeQuantiles(exprs(expressionSetGcrma), ties=TRUE)
> subGroup <- pData(expressionSetGcrma)$subGroup
> design <- model.matrix(~ -1 +factor(subGroup ))
>
> colnames(design) <- c("group1", "group2")
> contrast.matrix <- makeContrasts(group1-group2, levels=design)
> fit <- lmFit(normDat,design)
> fit2 <- contrasts.fit(fit, contrast.matrix)
> fit2 <- eBayes(fit2)
> normDat.p <- fit2$p.value
>
> normDat.p[1:5]
[1] 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761
> #[1] 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761
>
> system.time(goGeneSet <- getGeneSets(species = "Mouse", geneSetSource = "GOBP", entrezIdentifiers = featureNames(expressionSetGcrma)))
Loading required package: GO.db
user system elapsed
30.07 1.41 31.47
> goGeneSet[1:3]
$`GO:0000002`
[1] "11545" "16882" "17258" "17527" "19017" "21975" "22059" "23797"
[9] "27393" "27395" "27397" "50776" "57813" "70556" "72170" "72962"
[17] "74143" "74528" "83408" "192287" "216021" "216805" "229524" "230784"
[25] "327762"
$`GO:0000003`
[1] "11287" "11352" "11421" "11430" "11434" "11441"
[7] "11477" "11479" "11480" "11486" "11495" "11497"
[13] "11504" "11516" "11517" "11535" "11551" "11552"
[19] "11553" "11576" "11600" "11606" "11614" "11622"
[25] "11625" "11643" "11647" "11651" "11674" "11705"
[31] "11747" "11757" "11789" "11797" "11804" "11819"
[37] "11820" "11835" "11839" "11857" "11863" "11865"
[43] "11883" "11920" "11998" "12009" "12018" "12028"
[49] "12034" "12043" "12048" "12050" "12053" "12124"
[55] "12125" "12142" "12155" "12159" "12160" "12161"
[61] "12162" "12163" "12164" "12166" "12167" "12168"
[67] "12173" "12190" "12192" "12211" "12235" "12236"
[73] "12237" "12261" "12290" "12305" "12310" "12316"
[79] "12317" "12323" "12344" "12363" "12366" "12380"
[85] "12387" "12394" "12411" "12416" "12426" "12427"
[91] "12443" "12447" "12448" "12449" "12458" "12461"
[97] "12462" "12464" "12465" "12466" "12468" "12469"
[103] "12505" "12527" "12530" "12531" "12532" "12550"
[109] "12566" "12576" "12577" "12589" "12591" "12592"
[115] "12593" "12606" "12608" "12617" "12638" "12640"
[121] "12659" "12702" "12704" "12705" "12745" "12753"
[127] "12767" "12801" "12804" "12841" "12846" "12877"
[133] "12916" "12918" "12919" "12929" "12946" "12977"
[139] "12981" "13006" "13030" "13039" "13046" "13052"
[145] "13070" "13075" "13123" "13134" "13164" "13166"
[151] "13205" "13206" "13363" "13382" "13383" "13393"
[157] "13404" "13411" "13435" "13487" "13488" "13491"
[163] "13492" "13498" "13524" "13525" "13526" "13529"
[169] "13615" "13617" "13618" "13649" "13653" "13667"
[175] "13731" "13813" "13819" "13852" "13854" "13856"
[181] "13857" "13866" "13870" "13874" "13875" "13982"
[187] "13983" "13984" "14008" "14011" "14087" "14088"
[193] "14155" "14160" "14165" "14178" "14179" "14180"
[199] "14183" "14211" "14228" "14238" "14276" "14283"
[205] "14308" "14309" "14313" "14366" "14367" "14388"
[211] "14421" "14431" "14447" "14453" "14460" "14461"
[217] "14462" "14463" "14531" "14536" "14566" "14595"
[223] "14598" "14609" "14610" "14620" "14622" "14632"
[229] "14633" "14654" "14658" "14682" "14705" "14714"
[235] "14725" "14748" "14764" "14766" "14782" "14784"
[241] "14810" "14815" "14824" "15013" "15018" "15078"
[247] "15081" "15110" "15182" "15194" "15204" "15205"
[253] "15211" "15212" "15213" "15214" "15221" "15235"
[259] "15247" "15251" "15270" "15361" "15364" "15373"
[265] "15375" "15377" "15378" "15387" "15395" "15396"
[271] "15398" "15405" "15408" "15423" "15430" "15431"
[277] "15433" "15438" "15446" "15463" "15482" "15484"
[283] "15486" "15487" "15488" "15499" "15500" "15502"
[289] "15511" "15512" "15516" "15567" "15570" "15574"
[295] "15894" "15904" "16000" "16001" "16002" "16007"
[301] "16011" "16147" "16153" "16157" "16173" "16175"
[307] "16176" "16322" "16323" "16324" "16330" "16336"
[313] "16337" "16365" "16401" "16410" "16412" "16433"
[319] "16450" "16477" "16532" "16542" "16590" "16601"
[325] "16650" "16669" "16691" "16777" "16783" "16833"
[331] "16842" "16846" "16847" "16848" "16859" "16866"
[337] "16867" "16869" "16871" "16872" "16875" "16876"
[343] "16878" "16886" "16952" "16970" "16974" "17125"
[349] "17128" "17129" "17149" "17171" "17173" "17191"
[355] "17221" "17235" "17240" "17242" "17256" "17283"
[361] "17289" "17295" "17300" "17304" "17311" "17319"
[367] "17345" "17350" "17381" "17390" "17395" "17427"
[373] "17450" "17451" "17535" "17684" "17685" "17686"
[379] "17687" "17688" "17701" "17702" "17761" "17771"
[385] "17776" "17836" "17864" "17886" "17977" "17978"
[391] "17979" "17986" "18000" "18004" "18005" "18011"
[397] "18014" "18022" "18072" "18095" "18119" "18121"
[403] "18127" "18128" "18129" "18142" "18159" "18168"
[409] "18194" "18211" "18285" "18286" "18291" "18292"
[415] "18387" "18413" "18417" "18426" "18429" "18430"
[421] "18431" "18436" "18441" "18442" "18472" "18475"
[427] "18476" "18504" "18507" "18514" "18551" "18552"
[433] "18555" "18591" "18595" "18606" "18617" "18663"
[439] "18667" "18671" "18747" "18749" "18763" "18764"
[445] "18766" "18775" "18776" "18783" "18787" "18791"
[451] "18792" "18793" "18795" "18799" "18802" "18811"
[457] "18812" "18814" "18815" "18817" "18830" "18858"
[463] "18861" "18952" "19014" "19015" "19016" "19049"
[469] "19052" "19059" "19090" "19109" "19110" "19111"
[475] "19112" "19113" "19114" "19116" "19118" "19119"
[481] "19120" "19143" "19156" "19183" "19204" "19211"
[487] "19214" "19215" "19219" "19223" "19225" "19229"
[493] "19242" "19247" "19275" "19288" "19294" "19317"
[499] "19339" "19355" "19357" "19359" "19360" "19361"
[505] "19366" "19401" "19411" "19662" "19664" "19701"
[511] "19725" "19733" "19735" "19773" "19821" "19886"
[517] "20017" "20104" "20112" "20181" "20182" "20315"
[523] "20317" "20319" "20322" "20346" "20363" "20377"
[529] "20397" "20415" "20423" "20437" "20474" "20475"
[535] "20520" "20541" "20613" "20655" "20662" "20671"
[541] "20674" "20675" "20681" "20682" "20683" "20686"
[547] "20687" "20690" "20708" "20719" "20720" "20724"
[553] "20729" "20730" "20732" "20733" "20744" "20758"
[559] "20779" "20826" "20843" "20848" "20850" "20851"
[565] "20860" "20869" "20871" "20873" "20878" "20892"
[571] "20897" "20899" "20905" "20910" "20957" "20962"
[577] "20997" "21336" "21337" "21338" "21357" "21386"
[583] "21405" "21410" "21412" "21414" "21416" "21425"
[589] "21454" "21463" "21645" "21674" "21679" "21744"
[595] "21749" "21803" "21808" "21812" "21821" "21823"
[601] "21824" "21830" "21833" "21834" "21843" "21849"
[607] "21857" "21869" "21887" "21923" "21945" "21958"
[613] "21959" "21973" "21974" "22022" "22026" "22061"
[619] "22064" "22065" "22068" "22092" "22113" "22114"
[625] "22115" "22127" "22137" "22174" "22187" "22209"
[631] "22210" "22215" "22249" "22329" "22334" "22337"
[637] "22339" "22353" "22371" "22384" "22412" "22413"
[643] "22415" "22417" "22418" "22421" "22422" "22431"
[649] "22441" "22445" "22446" "22589" "22632" "22635"
[655] "22661" "22668" "22691" "22694" "22696" "22697"
[661] "22698" "22701" "22702" "22762" "22764" "22768"
[667] "22786" "22787" "22788" "22789" "23793" "23885"
[673] "23920" "23950" "23967" "23968" "23980" "23991"
[679] "23997" "24061" "24084" "24086" "24127" "24128"
[685] "26357" "26362" "26366" "26370" "26380" "26384"
[691] "26395" "26407" "26413" "26416" "26417" "26423"
[697] "26434" "26437" "26564" "26900" "26909" "26910"
[703] "26927" "26934" "26942" "26946" "26972" "27061"
[709] "27083" "27084" "27206" "27222" "27354" "27356"
[715] "27372" "27386" "28036" "28078" "28088" "28105"
[721] "28114" "28135" "29871" "29876" "30054" "30841"
[727] "30939" "30953" "30959" "50500" "50501" "50505"
[733] "50525" "50722" "50785" "50790" "50796" "50878"
[739] "50915" "51789" "51792" "51885" "51938" "52020"
[745] "52028" "52679" "52683" "52864" "53381" "53419"
[751] "53422" "53424" "53601" "53604" "53614" "53814"
[757] "53878" "53885" "53897" "53975" "54003" "54004"
[763] "54137" "54140" "54204" "54383" "54388" "54418"
[769] "54427" "54486" "54524" "54562" "54608" "54611"
[775] "54650" "54725" "55925" "55978" "55993" "55994"
[781] "56092" "56094" "56096" "56213" "56218" "56220"
[787] "56223" "56228" "56274" "56291" "56312" "56334"
[793] "56335" "56371" "56406" "56436" "56449" "56484"
[799] "56503" "56523" "56526" "56635" "56693" "56710"
[805] "56711" "56717" "56739" "56746" "57256" "57264"
[811] "57320" "57746" "57749" "57815" "57816" "57908"
[817] "58186" "58226" "58230" "58231" "58864" "58991"
[823] "58998" "59030" "59083" "60530" "60534" "60597"
[829] "63872" "64009" "64335" "64383" "64707" "64931"
[835] "65247" "65971" "66197" "66313" "66392" "66404"
[841] "66515" "66573" "66634" "66654" "66707" "66712"
[847] "66713" "66720" "66722" "66793" "66923" "66977"
[853] "66983" "67000" "67010" "67030" "67042" "67077"
[859] "67121" "67141" "67181" "67204" "67231" "67310"
[865] "67331" "67333" "67345" "67378" "67402" "67504"
[871] "67505" "67555" "67561" "67652" "67690" "67713"
[877] "67753" "67869" "67909" "67946" "67968" "67981"
[883] "68107" "68166" "68170" "68231" "68265" "68275"
[889] "68298" "68328" "68549" "68708" "68767" "68911"
[895] "68922" "68981" "69032" "69064" "69260" "69286"
[901] "69287" "69306" "69307" "69310" "69376" "69444"
[907] "69538" "69546" "69707" "69716" "69852" "69865"
[913] "69928" "69982" "70069" "70093" "70099" "70231"
[919] "70235" "70248" "70375" "70441" "70465" "70503"
[925] "70691" "70772" "70840" "70862" "70873" "70891"
[931] "70918" "70956" "70977" "71062" "71089" "71099"
[937] "71132" "71175" "71241" "71242" "71371" "71567"
[943] "71709" "71711" "71765" "71830" "71836" "71840"
[949] "71846" "71854" "71904" "71914" "71950" "71981"
[955] "72135" "72148" "72162" "72236" "72415" "72469"
[961] "72504" "72508" "72568" "72634" "72780" "72787"
[967] "72891" "72938" "73242" "73244" "73296" "73316"
[973] "73329" "73336" "73412" "73456" "73472" "73542"
[979] "73616" "73673" "73679" "73721" "74041" "74068"
[985] "74075" "74090" "74117" "74174" "74188" "74229"
[991] "74237" "74267" "74286" "74288" "74297" "74309"
[997] "74354" "74360" "74369" "74386" "74401" "74434"
[1003] "74446" "74450" "74468" "74469" "74691" "74708"
[1009] "74716" "74754" "74847" "74927" "75019" "75033"
[1015] "75140" "75178" "75202" "75388" "75410" "75459"
[1021] "75469" "75514" "75533" "75571" "75596" "75605"
[1027] "75622" "75642" "75646" "75753" "75801" "75826"
[1033] "75828" "75909" "76378" "76407" "76486" "76499"
[1039] "76718" "76800" "76850" "76856" "76858" "76867"
[1045] "76915" "76925" "76943" "77053" "77128" "77424"
[1051] "77595" "77684" "77963" "77980" "78081" "78124"
[1057] "78284" "78619" "78634" "78658" "78784" "78801"
[1063] "78803" "78925" "80297" "80517" "80838" "80884"
[1069] "80912" "81018" "83456" "83557" "83558" "83560"
[1075] "83561" "83964" "83984" "93684" "93736" "93757"
[1081] "93759" "93760" "93837" "93960" "94221" "94224"
[1087] "94244" "94246" "97086" "97165" "98558" "98711"
[1093] "99412" "99929" "100121" "100155" "100317" "100535"
[1099] "100986" "101187" "101476" "102774" "103468" "103554"
[1105] "103733" "103768" "104083" "104111" "104148" "104156"
[1111] "104263" "104271" "104310" "104346" "104362" "104601"
[1117] "104799" "104806" "105349" "105511" "105988" "106389"
[1123] "106757" "107515" "107586" "107626" "107656" "107849"
[1129] "107970" "107995" "108829" "108961" "109685" "109689"
[1135] "109727" "109785" "110012" "110082" "110084" "110147"
[1141] "110355" "110459" "110542" "110957" "110958" "112405"
[1147] "114606" "114642" "114661" "114662" "114714" "114875"
[1153] "116837" "140498" "140557" "170676" "171285" "171429"
[1159] "171506" "191578" "192119" "192176" "192195" "192199"
[1165] "192897" "193838" "194908" "195434" "207165" "207304"
[1171] "207352" "207607" "207686" "208169" "208188" "208727"
[1177] "209091" "209351" "210510" "210529" "210554" "211064"
[1183] "211484" "211651" "212517" "212670" "212937" "213081"
[1189] "213236" "213272" "213389" "213541" "213742" "214105"
[1195] "214253" "214290" "214292" "214384" "214572" "214575"
[1201] "214593" "214901" "215028" "215029" "215095" "215387"
[1207] "215854" "216350" "216725" "216869" "217039" "217116"
[1213] "217325" "217715" "217716" "218214" "218454" "218914"
[1219] "223593" "223697" "223825" "223921" "223989" "224045"
[1225] "224171" "224661" "224727" "224826" "224902" "225182"
[1231] "225865" "226090" "226162" "226265" "226841" "227210"
[1237] "227394" "227615" "227631" "227736" "228421" "228980"
[1243] "229227" "229357" "229700" "230103" "230126" "230594"
[1249] "230809" "230861" "230899" "231051" "231386" "231633"
[1255] "231672" "231832" "231912" "232174" "232223" "232286"
[1261] "232345" "232664" "233276" "233328" "234857" "235072"
[1267] "235320" "235559" "235626" "235628" "236266" "236899"
[1273] "237336" "237625" "237911" "238055" "238057" "238247"
[1279] "238328" "238330" "239083" "239167" "239528" "239731"
[1285] "240069" "240255" "240590" "240697" "240725" "240899"
[1291] "241624" "242202" "242523" "243862" "243897" "243905"
[1297] "244551" "245000" "245865" "246747" "252828" "252868"
[1303] "252967" "252973" "259279" "260305" "264134" "268396"
[1309] "268420" "268465" "268491" "268591" "268697" "268755"
[1315] "268860" "268903" "268930" "269254" "269275" "269610"
[1321] "269682" "269701" "270624" "271036" "271127" "271639"
[1327] "272643" "276920" "277353" "278240" "280287" "280667"
[1333] "280668" "317653" "319177" "319448" "319953" "320022"
[1339] "320244" "320277" "320558" "320752" "320790" "327826"
[1345] "328019" "328365" "328401" "328440" "328580" "328845"
[1351] "329557" "329954" "330149" "330188" "330319" "330409"
[1357] "330470" "330830" "330890" "331046" "331416" "332110"
[1363] "378430" "378462" "380654" "380684" "380702" "380709"
[1369] "380773" "380855" "380993" "380994" "381022" "381157"
[1375] "381196" "381290" "381404" "381489" "381677" "381759"
[1381] "382077" "382217" "382275" "382277" "382301" "383491"
[1387] "384619" "387139" "387140" "387153" "387156" "387161"
[1393] "387162" "387177" "387178" "387179" "387188" "387198"
[1399] "387218" "387244" "387245" "387246" "387247" "399599"
[1405] "433700" "434438" "434784" "434794" "442829" "545156"
[1411] "546118" "546272" "546282" "574428" "574437" "574438"
[1417] "619517" "619697" "619991" "622554" "623474" "625249"
[1423] "625662" "627081" "629389" "664799" "664829" "665187"
[1429] "665270" "665780" "666317" "666528" "668110" "668929"
[1435] "671232" "671564" "723849" "723868" "723886" "723932"
[1441] "723939" "723955" "723956" "723962" "723965" "723966"
[1447] "735262" "735309" "751535" "100009600" "100038417" "100038489"
[1453] "100038977" "100039030" "100039065" "100039120" "100039842" "100039905"
[1459] "100040483" "100040608" "100040894" "100042109" "100042175" "100042922"
[1465] "100042929" "100042931" "100042939" "100042943" "100042944" "100042946"
[1471] "100043216" "100048534" "100049545" "100049546" "100049548" "100113365"
[1477] "100124460" "100124479" "100124480" "100190765" "100270744" "100504642"
[1483] "100861637" "100861881" "101055773" "101056116" "101056210" "102443351"
[1489] "102631559" "102632183" "102633564" "102636501" "102638101" "102638793"
[1495] "102639094" "102639490" "102639895" "105247282" "108168552" "108168557"
[1501] "108168582" "108168594" "113523646"
$`GO:0000012`
[1] "11545" "14211" "22064" "22594" "66408" "70099" "72103" "93759"
[9] "104884" "319583"
> # output changes with annotation version !
>
> y <- normDat.p[,1]
> names(y) <- featureNames(expressionSetGcrma)
>
> y[1:10]
100009600 100012 100017 100019 100034251 100036521 100037258 100037278
0.4328583 0.7448996 0.6088859 0.1845008 0.2312761 0.7865153 0.7772888 0.1037431
100038570 100038635
0.1368744 0.3272610
> # 100009600 100012 100017 100019 100034251 100036521 100037258 100037278
> # 0.4328583 0.7448996 0.6088859 0.1845008 0.2312761 0.7865153 0.7772888 0.1037431
> # 100038570 100038635
> # 0.1368744 0.3272610
>
> mlpObject <- MLP(geneSet = goGeneSet, geneStatistic = y, minGenes = 5, maxGenes = 100, rowPermutations = TRUE,
+ nPermutations = 6, smoothPValues = TRUE)
>
>
>
> mlpObject[1:10, ]
totalGeneSetSize testedGeneSetSize geneSetStatistic geneSetPValue
GO:0002282 5 5 1.6379883 0.0001425143
GO:1900426 12 10 1.1666016 0.0003970342
GO:0019886 14 14 1.0549211 0.0004675798
GO:0060179 12 10 1.1332820 0.0006140852
GO:1900424 19 17 0.9799674 0.0007850341
GO:0002468 11 9 1.1429532 0.0008683572
GO:0002495 19 19 0.9388391 0.0010271824
GO:0002478 25 24 0.8798107 0.0010911776
GO:1903334 6 5 1.3744357 0.0012863305
GO:0002504 20 20 0.9113723 0.0013290942
geneSetDescription
GO:0002282 microglial cell activation involved in immune response
GO:1900426 positive regulation of defense response to bacterium
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0060179 male mating behavior
GO:1900424 regulation of defense response to bacterium
GO:0002468 dendritic cell antigen processing and presentation
GO:0002495 antigen processing and presentation of peptide antigen via MHC class II
GO:0002478 antigen processing and presentation of exogenous peptide antigen
GO:1903334 positive regulation of protein folding
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
> # output changes with annotation version !
>
> plotGOgraph(object = mlpObject, main = "test of main")
Loading required package: Rgraphviz
Loading required package: graph
Loading required package: grid
Attaching package: 'Rgraphviz'
The following objects are masked from 'package:IRanges':
from, to
The following objects are masked from 'package:S4Vectors':
from, to
Loading required package: GOstats
Loading required package: Category
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Attaching package: 'GOstats'
The following object is masked from 'package:AnnotationDbi':
makeGOGraph
Loading required package: annotate
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
Attaching package: 'annotate'
The following object is masked from 'package:Rgraphviz':
toFile
>
> pdf(file = "test10.pdf", width = 10, height = 10)
> # x11(width = 10, height = 10)
> plot(mlpObject, nRow = 10) # by default: type = "barplot"
> dev.off()
pdf
2
>
> unlink("test10.pdf")
>
> if (FALSE){
+ pdf(file = "test5.pdf", width =10, height = 10)
+ mlpBarplot(object = mlpObject, geneSetSource = "GOBP", nRow = 10, descriptionLength = 5)
+ dev.off()
+
+ unlink("test5.pdf")
+
+ pdf(file = "test100.pdf", width =10, height = 20)
+ mlpBarplot(object = mlpObject, geneSetSource = "GOBP", nRow = 10, descriptionLength = 100)
+ dev.off()
+
+ unlink("test100.pdf")
+ }
>
> plot(mlpObject, type = "quantileCurves")
> plot(mlpObject, type = "GOgraph")
>
> proc.time()
user system elapsed
56.35 1.84 59.18
|
