| Previous changeset 9:19ea355e26b3 (2017-02-28) Next changeset 11:983651783ce9 (2017-03-22) |
|
Commit message:
Uploaded |
|
added:
getGEO/.Rhistory getGEO/._.DS_Store getGEO/getGEO.R getGEO/getGEO.xml getGEO/test-data/._.DS_Store getGEO/test-data/._input.csv getGEO/test-data/IlmnTable.txt getGEO/test-data/MetaTable.txt getGEO/test-data/gmTable.txt getGEO/test-data/input.csv getGEO/tool_dependencies.xml |
|
removed:
GEO/.Rhistory GEO/._.DS_Store GEO/getGEO.R GEO/getGEO.xml GEO/test-data/._.DS_Store GEO/test-data/._input.csv GEO/test-data/IlmnTable.txt GEO/test-data/MetaTable.txt GEO/test-data/gmTable.txt GEO/test-data/input.csv GEO/tool_dependencies.xml |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 GEO/.Rhistory --- a/GEO/.Rhistory Tue Feb 28 05:11:54 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -??options -options(warn = -1) -+options("download.file.method"="wget") -options("download.file.method"="wget") -options(warn = -1,"download.file.method"="wget") -??getPlatform -??getPlatform |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 GEO/._.DS_Store |
| b |
| Binary file GEO/._.DS_Store has changed |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 GEO/getGEO.R --- a/GEO/getGEO.R Tue Feb 28 05:11:54 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,54 +0,0 @@ -require("BiocGenerics", quietly = TRUE) -require("data.table", quietly = TRUE) -require("GEOquery", quietly = TRUE) -require("rtracklayer", quietly = TRUE) -require("FDb.InfiniumMethylation.hg19", quietly = TRUE) - -options("download.file.method.GEOquery"="wget") -options(warn = -1) - -args <- commandArgs(trailingOnly = TRUE) -GSMTable = args[1] -protocol = args[2] -platform = args[3] -Data_Table = args[4] - -TAB = fread(GSMTable) - -if (is.null(TAB)) { - stop("Must specify input files") -} else { - GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE) - IlmnIDTable <- Table(GEODataTable) - MetaData <- data.frame(Meta(GEODataTable)) - - - write.table(MetaData, protocol, row.names = FALSE, sep = "\t") -} - -hm450.hg19 <- getPlatform() - -IlmnInfo <- - data.table( - IlmnID = names(hm450.hg19), - CHR = as.data.frame(hm450.hg19@seqnames)$value, - BP = as.numeric(hm450.hg19@elementMetadata$probeStart) - ) - - -write.table(IlmnInfo, platform, row.names = FALSE, sep = "\t") - - -if (length(TAB$ID) > 1) { - mysamples <- - do.call("data.table", lapply(TAB$ID[-1], function(x) - Table(getGEO(x, getGPL = FALSE))[, -1])) - - gmSet <- data.table(IlmnIDTable[, -1], mysamples) - -} else { - gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE)) -} - -write.table(gmSet, Data_Table, row.names = FALSE,quote=FALSE,sep="\t") - |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 GEO/getGEO.xml --- a/GEO/getGEO.xml Tue Feb 28 05:11:54 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,39 +0,0 @@ -<tool id="GEO" name="getGEO" version="1.16.2"> - <requirements> - <requirement type="package" version="3.2.1">R</requirement> - </requirements> -<stdio> - <exit_code range="1:" /> - </stdio> - <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$protocol" "$platform" "$Data_Table"</command> - <inputs> - <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable"> - <validator type="empty_field" message="This field is required."/> - </param> - </inputs> - <outputs> - <data format="txt" name="protocol" label="protocol.txt"/> - <data format="txt" name="platform" label="platform.txt"/> - <data format="txt" name="Data_Table" label="Data_Table.txt"/> - </outputs> - <tests> - <test> - <param name="test"> - <element name="test-data"> - <collection type="data"> - <element name="GSMTable" value="test-data/input.csv" /> - </collection> - </element> - </param> - <output format="txt" name="protocol" label="test-data/protocol.txt"/> - <output format="txt" name="platform" label="test-data/platform.txt"/> - <output format="txt" name="Data_Table" label="test-data/Data_Table.txt"/> - </test> - </tests> - <help> -**Description** -</help> -<citations> -GEO -</citations> -</tool> |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 GEO/test-data/._.DS_Store |
| b |
| Binary file GEO/test-data/._.DS_Store has changed |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 GEO/test-data/._input.csv |
| b |
| Binary file GEO/test-data/._input.csv has changed |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 GEO/test-data/IlmnTable.txt --- a/GEO/test-data/IlmnTable.txt Tue Feb 28 05:11:54 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,485578 +0,0 @@\n-"IlmnID","CHR","BP"\n-"cg04913815","chr16",60438\n-"cg01686861","chr16",60700\n-"cg05558259","chr16",61037\n-"cg26978960","chr16",62412\n-"cg03792876","chr16",73195\n-"cg09699726","chr16",91554\n-"cg07549526","chr16",91663\n-"cg02851049","chr16",101212\n-"cg11876012","chr16",101638\n-"cg14820573","chr16",102073\n-"cg14747225","chr16",102976\n-"cg16670573","chr16",103375\n-"cg09499248","chr16",103483\n-"cg00762468","chr16",103568\n-"cg05055400","chr16",103592\n-"cg09969830","chr16",103646\n-"cg00958578","chr16",103715\n-"cg11653271","chr16",103723\n-"cg01188584","chr16",103853\n-"cg03974483","chr16",103985\n-"cg08718695","chr16",104135\n-"cg01062126","chr16",104539\n-"cg00992207","chr16",107404\n-"cg00914902","chr16",108066\n-"cg27248189","chr16",110257\n-"cg06194960","chr16",111362\n-"cg07608562","chr16",111610\n-"cg20220196","chr16",111753\n-"cg09201525","chr16",111823\n-"cg03333116","chr16",112396\n-"cg04721268","chr16",112802\n-"cg01403103","chr16",112804\n-"cg01502407","chr16",113107\n-"cg04322210","chr16",114987\n-"cg26933686","chr16",115957\n-"cg00179196","chr16",117934\n-"cg07405083","chr16",119384\n-"cg06934747","chr16",120902\n-"cg00525011","chr16",122031\n-"cg03948744","chr16",122515\n-"cg00079891","chr16",122716\n-"cg09113560","chr16",122764\n-"cg04995976","chr16",123198\n-"cg06230303","chr16",123353\n-"cg01262217","chr16",123363\n-"cg04260507","chr16",123553\n-"cg17199481","chr16",123676\n-"cg01422009","chr16",125896\n-"cg03462322","chr16",126397\n-"cg16383109","chr16",126403\n-"cg03110993","chr16",126800\n-"cg03492469","chr16",126855\n-"cg05501742","chr16",126844\n-"cg16003913","chr16",127072\n-"cg04257263","chr16",127088\n-"cg15017278","chr16",127401\n-"cg02729269","chr16",127772\n-"cg07395378","chr16",127904\n-"cg01609171","chr16",127949\n-"cg10009236","chr16",127968\n-"cg05397937","chr16",128446\n-"cg15768556","chr16",128630\n-"cg05394456","chr16",129230\n-"cg10143220","chr16",129454\n-"cg00935108","chr16",129562\n-"cg02949481","chr16",131514\n-"cg05791870","chr16",136656\n-"cg07484220","chr16",136761\n-"cg07405534","chr16",139691\n-"cg26925590","chr16",139704\n-"cg07371452","chr16",139732\n-"cg04807152","chr16",147558\n-"cg16730559","chr16",157323\n-"cg02353723","chr16",163133\n-"cg09430181","chr16",175615\n-"cg02028423","chr16",185078\n-"cg01527023","chr16",188138\n-"cg00928894","chr16",188221\n-"cg02369618","chr16",188603\n-"cg09580244","chr16",188684\n-"cg02783232","chr16",188741\n-"cg08524197","chr16",188802\n-"cg02855078","chr16",188815\n-"cg08969593","chr16",188855\n-"cg06171619","chr16",188884\n-"cg00389577","chr16",189052\n-"cg24399405","chr16",189577\n-"cg27009501","chr16",192791\n-"cg06929449","chr16",199366\n-"cg10317591","chr16",199773\n-"cg08957279","chr16",202263\n-"cg10164238","chr16",202320\n-"cg21960110","chr16",202434\n-"cg01839639","chr16",202542\n-"cg25425005","chr16",202905\n-"cg07263153","chr16",202926\n-"cg08400316","chr16",204221\n-"cg02279719","chr16",204474\n-"cg06459847","chr16",204601\n-"cg07498624","chr16",204783\n-"cg01923692","chr16",204949\n-"cg06031493","chr16",210205\n-"cg05390075","chr16",210528\n-"cg07067950","chr16",212416\n-"cg07893512","chr16",214728\n-"cg05057452","chr16",214922\n-"cg25322095","chr16",215002\n-"cg07466193","chr16",215362\n-"cg01744019","chr16",215545\n-"cg09812623","chr16",215733\n-"cg08393070","chr16",215743\n-"cg01558909","chr16",215797\n-"cg26540367","chr16",215816\n-"cg06319822","chr16",215912\n-"cg26976732","chr16",216052\n-"cg21664030","chr16",216244\n-"cg04141813","chr16",216450\n-"cg03309232","chr16",216626\n-"cg12251336","chr16",216719\n-"cg09523819","chr16",216709\n-"cg04321267","chr16",219107\n-"cg04377849","chr16",221536\n-"cg26637826","chr16",221542\n-"cg04938149","chr16",221811\n-"cg15597257","chr16",222837\n-"cg00697413","chr16",222858\n-"cg16263182","chr16",223351\n-"cg05956679","chr16",223360\n-"cg01319583","chr16",224880\n-"cg01704105","chr16",225666\n-"cg08923033","chr16",226002\n-"cg06235582","chr16",226668\n-"cg27452732","chr16",226670\n-"cg10647513","chr16",227155\n-"cg09434193","chr16",227185\n-"cg08923355","chr16",227469\n-"cg05933901","chr16'..b'16637094\n-"cg09804407","chrY",16733251\n-"cg08816194","chrY",16733442\n-"cg07795413","chrY",16733930\n-"cg01073572","chrY",16924422\n-"cg01498999","chrY",16939335\n-"cg03278611","chrY",16941543\n-"cg09300505","chrY",16942106\n-"cg05939513","chrY",16942232\n-"cg02340092","chrY",16945913\n-"cg25667057","chrY",17567474\n-"cg23834181","chrY",17567486\n-"cg03672679","chrY",17567897\n-"cg04792227","chrY",17568097\n-"cg00679624","chrY",17568445\n-"cg20764275","chrY",17568616\n-"cg14742615","chrY",17569363\n-"cg01882666","chrY",17571429\n-"cg03905640","chrY",19625260\n-"cg01209756","chrY",19671414\n-"cg17115812","chrY",19678480\n-"cg14151065","chrY",19678487\n-"cg25012987","chrY",19691491\n-"cg16292375","chrY",19691502\n-"cg16894943","chrY",20488221\n-"cg06060201","chrY",20488232\n-"cg04170994","chrY",20488245\n-"cg09408193","chrY",20501241\n-"cg10252249","chrY",20508275\n-"cg23308414","chrY",20508314\n-"cg26046487","chrY",20736099\n-"cg10646950","chrY",20748734\n-"cg00479827","chrY",21036938\n-"cg10691859","chrY",21041339\n-"cg15281205","chrY",21100424\n-"cg05230942","chrY",21155222\n-"cg13765957","chrY",21208573\n-"cg26251715","chrY",21236181\n-"cg03244189","chrY",21238424\n-"cg13845521","chrY",21238886\n-"cg10811597","chrY",21239219\n-"cg11816202","chrY",21239284\n-"cg00212031","chrY",21239300\n-"cg15345074","chrY",21239413\n-"cg11684211","chrY",21239559\n-"cg06628792","chrY",21240004\n-"cg00121626","chrY",21664248\n-"cg15027426","chrY",21664556\n-"cg00876332","chrY",21664717\n-"cg15794778","chrY",21664973\n-"cg09228985","chrY",21666030\n-"cg06065495","chrY",21666261\n-"cg03533500","chrY",21668372\n-"cg06231362","chrY",21726406\n-"cg25756647","chrY",21728575\n-"cg06502680","chrY",21728904\n-"cg20864678","chrY",21728989\n-"cg14492024","chrY",21729001\n-"cg05725925","chrY",21729010\n-"cg05621349","chrY",21729021\n-"cg10076560","chrY",21729144\n-"cg15682993","chrY",21729203\n-"cg07731488","chrY",21729314\n-"cg05672930","chrY",21729555\n-"cg17660627","chrY",21729665\n-"cg14931215","chrY",21867654\n-"cg00308367","chrY",21868484\n-"cg27509967","chrY",21877683\n-"cg15329860","chrY",21906636\n-"cg25815185","chrY",21906868\n-"cg27049643","chrY",21906893\n-"cg26517491","chrY",21906895\n-"cg15662272","chrY",21906974\n-"cg02522936","chrY",22680010\n-"cg10799208","chrY",22681388\n-"cg26928789","chrY",22682345\n-"cg09081202","chrY",22735272\n-"cg01988452","chrY",22736480\n-"cg13308744","chrY",22736536\n-"cg10172760","chrY",22736785\n-"cg10620659","chrY",22737343\n-"cg15422579","chrY",22737376\n-"cg15059553","chrY",22737505\n-"cg01644972","chrY",22737508\n-"cg02233190","chrY",22737591\n-"cg26983535","chrY",22737594\n-"cg11225091","chrY",22737615\n-"cg03750315","chrY",22737848\n-"cg02884332","chrY",22737946\n-"cg08715207","chrY",22737921\n-"cg08820785","chrY",22738029\n-"cg10593480","chrY",22738723\n-"cg00063477","chrY",22741795\n-"cg01900066","chrY",22754881\n-"cg07747963","chrY",22917039\n-"cg10841270","chrY",22917104\n-"cg01943289","chrY",22917296\n-"cg17741448","chrY",22917782\n-"cg02012379","chrY",22917846\n-"cg00676506","chrY",22917913\n-"cg06322277","chrY",22917937\n-"cg26058907","chrY",22917894\n-"cg02050847","chrY",22918038\n-"cg14029254","chrY",22918213\n-"cg02352633","chrY",23561638\n-"cg03416979","chrY",23566240\n-"cg05051262","chrY",23566524\n-"cg25427172","chrY",23566730\n-"cg10666546","chrY",23566863\n-"cg25640065","chrY",23569324\n-"cg16552926","chrY",23694843\n-"cg25918849","chrY",23753284\n-"cg11021362","chrY",23756676\n-"cg14467015","chrY",23757241\n-"cg15516537","chrY",24036834\n-"cg05999368","chrY",24044030\n-"cg15462332","chrY",24052484\n-"cg26497631","chrY",24331310\n-"cg06865724","chrY",24445690\n-"cg25914522","chrY",24452543\n-"cg13808036","chrY",24453658\n-"cg10267609","chrY",24453709\n-"cg00335297","chrY",24454479\n-"cg03827298","chrY",24454879\n-"cg26983430","chrY",24549675\n-"cg22051787","chrY",24549677\n-"cg01757887","chrY",25114762\n-"cg00061679","chrY",25314123\n-"cg03930849","chrY",26716241\n-"cg17939569","chrY",27009430\n-"cg13365400","chrY",27210334\n-"cg21106100","chrY",28555488\n-"cg08265308","chrY",28555502\n-"cg14273923","chrY",28555912\n' |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 GEO/test-data/MetaTable.txt --- a/GEO/test-data/MetaTable.txt Tue Feb 28 05:11:54 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -"channel_count","characteristics_ch1","contact_address","contact_city","contact_country","contact_department","contact_institute","contact_name","contact_zip.postal_code","data_processing","data_row_count","description","extract_protocol_ch1","geo_accession","hyb_protocol","label_ch1","label_protocol_ch1","last_update_date","molecule_ch1","organism_ch1","platform_id","scan_protocol","series_id","source_name_ch1","status","submission_date","supplementary_file","taxid_ch1","title","type" -"1","sample type: melanoma cell line","Barngatan 2B","Lund","Sweden","Dept of Oncology","Lund University","Martin,,Lauss","22185","Raw intensities for methylated (M) and unmethylated (U) signal were extracted from Illumina’s GenomeStudio. Beta-values were calculated as M/(M+U). A total of 496 missing values (melanomas) were imputed using k-nearest neighbor imputation (k=10). For each sample we performed a peak-based correction of Illumina I and II chemical assays. For both assays we smoothed the beta values (Epanechnikov smoothing kernel) to estimate unmethylated and methylated peaks, respectively; and the unmethylated peak was moved to 0 and the methylated peak to 1 using linear scaling, with beta-values in between stretched accordingly. Beta-values below 0 were set back to 0 and values above 1 were set to 1.","485577","melanoma cell line","Genomic DNA was extracted from the biopsies using QIAamp DNA Mini Kit (Qiagen). A total of 500 ng of DNA were used for bisulfite treatment, using the EZ DNA Methylation Kit (Zymo). We hybridized 200 ng in 4 μl to the Infinium Human Methylation450 BeadChip array.","GSM1247787","Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol","Cy5 and Cy3","Standard Illumina Protocol","May 17 2015","genomic DNA","Homo sapiens","GPL13534","Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting","GSE51547","SKMEL3","Public on May 17 2015","Oct 22 2013","NONE","9606","genomic DNA from Sample SKMEL3","genomic" |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 GEO/test-data/gmTable.txt --- a/GEO/test-data/gmTable.txt Tue Feb 28 05:11:54 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,485578 +0,0 @@\n-"V1","V1","V2"\n-0.509,0.716,0.395\n-0.647,0.561,0.372\n-0.83,0.52,0.559\n-0.618,0.698,0.573\n-0.37,0.216,0.522\n-0.464,0.219,0.62\n-0.421,0.607,0.639\n-0.425,0.379,0.602\n-0,0,0\n-0.555,0.559,0.611\n-0.327,0.357,0.387\n-0.8,0.683,0.398\n-0.418,0.154,0.614\n-0.538,0.469,0.409\n-0.312,0.167,0.473\n-0.261,0.351,0.584\n-0.591,0.622,0.521\n-0.52,0.469,0.639\n-0.595,1,0.639\n-0.535,0.774,0.403\n-0.342,0.387,0.502\n-0.801,0.72,0.726\n-0.581,0.748,0.867\n-0.445,0.567,0.553\n-0.699,0.532,0.498\n-0.446,0.411,0.335\n-0.62,0.363,0.37\n-0.82,0.368,0.717\n-0.997,0,0.58\n-0.355,0.447,0.543\n-0.443,0.434,0.574\n-0.004,0,0.007\n-0.482,0.427,0.663\n-0.841,0.94,0.615\n-0.76,0.624,0.878\n-0.787,0.847,0.511\n-0.887,0.893,0.789\n-0.553,0.521,0.607\n-0.468,0.502,0.387\n-0.693,0.609,0.403\n-0.545,0.643,0.623\n-0.765,0.567,0.202\n-0.438,0.334,0.362\n-0.612,0.625,0.627\n-0.735,0.651,0.699\n-0.747,0.441,0.666\n-0.536,0.536,0.429\n-0.22,0.184,0.543\n-0.538,0.297,0.289\n-0.403,0.74,0.725\n-0.484,0.495,0.369\n-0.223,0.172,0.323\n-0.486,0.436,0.416\n-0.49,0.273,0.557\n-0.691,0.62,0.311\n-0.192,0.437,0.469\n-0.536,0.242,0.585\n-0.357,0.464,0.573\n-0.465,0.497,0.441\n-0.615,0.336,0.466\n-0,1,0.504\n-0.044,0.001,0.074\n-0.242,0.232,0.39\n-0.862,0.789,0.598\n-0.761,0.014,0.614\n-0.332,0.545,0.567\n-0.532,0.47,0.31\n-0.486,0.293,0.493\n-0.235,0.21,0.348\n-0,0,0.011\n-0,0,0\n-0.858,0.531,0.504\n-0.584,0.531,0.532\n-0.255,0.223,0.426\n-0.37,0.451,0.581\n-0.404,0.321,0.39\n-0.154,0.072,0.151\n-0.696,0.646,0.591\n-0.354,0.235,0.708\n-0.598,0.242,0.62\n-0.321,0.494,0.507\n-0.316,0.292,0.395\n-0.722,0.577,0.616\n-0.289,0.075,0.4\n-0.316,0.529,0.536\n-0.523,0.608,0.429\n-0.552,0.302,0.244\n-1,0.032,0.401\n-0.587,1,0.261\n-0.201,0.177,0.173\n-0.459,0.388,0.387\n-0.219,0.611,0.739\n-0.395,0.638,0.593\n-0.4,0.225,0.681\n-0.271,0.406,0.339\n-0.361,0.251,0.434\n-1,0,0.643\n-0.922,0.489,0.496\n-0.431,0.592,0.608\n-0.677,0.335,0.557\n-0.235,0.213,0.391\n-0.446,0.109,0.39\n-0.474,0.394,0.326\n-1,0,0.409\n-0.415,0.553,0.569\n-0.476,0.685,0.669\n-0.538,0.913,0.36\n-0.531,0.489,0.568\n-0.278,0.313,0.441\n-0.303,0.381,0.589\n-0.366,0.594,0.711\n-0.908,0.754,0.667\n-0,0,0.049\n-0.474,0.607,0.469\n-0.704,0.725,0.601\n-0.857,0.494,0.675\n-0.395,0.571,0.62\n-0.877,0.739,0.484\n-0.687,0.458,0.486\n-0.538,0.308,0.39\n-0.269,0.295,0.508\n-0.343,0.222,0.327\n-1,0.139,0.807\n-0.946,0.005,0.716\n-0.328,0.321,0.362\n-0.516,0.453,0.53\n-0.273,0.153,0.492\n-0.284,0.192,0.293\n-0.284,0.429,0.719\n-0.628,0.748,0.405\n-0.307,0.364,0.282\n-0.404,0.521,0.561\n-0.492,0.776,0.56\n-0.445,0.554,0.382\n-0.395,0.523,0.479\n-0.335,0.594,0.775\n-0.77,0.051,0.359\n-0.53,0.286,0.712\n-0.595,0.776,0.513\n-0.638,0.743,0.691\n-0.181,0.158,0.477\n-0.673,0.522,0.39\n-0.987,0.058,0.463\n-0.502,0.251,0.403\n-0.423,0.63,0.597\n-0.311,0.376,0.348\n-0.693,0.424,0.398\n-0.664,0.545,0.465\n-0.539,0.303,0.403\n-0.537,0.443,0.467\n-0.577,0.414,0.518\n-0.488,0.395,0.234\n-0.531,0.396,0.394\n-0.437,0.399,0.353\n-0.438,0.567,0.391\n-0.261,0.235,0.504\n-0.365,0.466,0.333\n-0.661,0.238,0.449\n-0.696,0.71,0.464\n-0.348,0.327,0.371\n-0.035,0.08,0.551\n-0.368,0.3,0.497\n-0.696,0.577,0.532\n-0.618,0.362,0.536\n-0.634,0.791,0.525\n-0.614,0.309,0.54\n-0.357,0.411,0.464\n-0.346,0.198,0.619\n-0.518,0.42,0.384\n-0.274,0.525,0.643\n-0.447,0.371,0.376\n-0.313,0.579,0.429\n-0.327,0.299,0.458\n-0.458,0.396,0.426\n-0.541,0.475,0.464\n-0.457,0.461,0.77\n-0.439,0.497,0.523\n-0.674,0.436,0.635\n-0.223,0.159,0.643\n-0.639,0.507,0.563\n-0.719,0.559,0.421\n-0.543,0.399,0.306\n-1,0.462,0.73\n-0.382,0.625,0.536\n-0.513,0.311,0.479\n-0.37,0.387,0.383\n-0.485,0.439,0.319\n-0.434,0.348,0.515\n-0.418,0.551,0.464\n-0.369,0.42,0.619\n-0.853,0.504,0.842\n-0.623,0.526,0.356\n-0.446,0.475,0.384\n-0.507,0.479,0.324\n-0.496,0.685,0.649\n-0.363,0.238,0.409\n-0.719,0.299,0.547\n-0.273,0.447,0.639\n-0.112,0.16,0.071\n-0.497,0.358,0.59\n-0.527,0.571,0.453\n-0.342,0.19,0.38\n-0.864,0.674,0.83\n-0.588,0.311,0.707\n-0.439,0.374,0.47\n-0.489,0.55,0.496\n-0.393,0.247,0.322\n-0.357,0.284,0.42\n-0.366,0.266,0.692\n-0.409,0.483,0.519\n-0.685,0.749,0.997\n-0.381,0.498,0.464\n-0.689,1,0.711\n-0.436,0.173,0.683\n-0.835,0.893,0.894\n-0.795,0.704,0.438\n-0.326,0.86'..b'0.506\n-0.031,0.006,0\n-0.458,0.043,0.127\n-0.948,0.914,0.945\n-0.015,0.018,0.012\n-1,1,0.851\n-0.734,0.536,0.645\n-0.961,0.961,0.556\n-0.027,0.026,0.003\n-0.817,0.54,0.802\n-0.981,0.963,1\n-0.65,0.599,0.856\n-0.144,0.195,0.138\n-0,0,0\n-0.023,0,0.006\n-0,0.067,0.003\n-0.984,0.868,0.901\n-0.084,0.074,0.428\n-0.952,0.838,1\n-0.025,0,0.036\n-0.002,0.315,0\n-0.236,0,0.295\n-0.29,0.125,0.446\n-0.677,0.452,0.004\n-0,0,0\n-0.002,0,0\n-0,0,0\n-0.974,0.873,0.877\n-0.903,0.572,0.654\n-0.295,0.095,0.096\n-0.906,0.795,0.64\n-0.035,0.019,0.015\n-1,0.52,0.705\n-0.929,0.874,0.67\n-0.699,0.126,0.684\n-0.992,0.961,0.608\n-0.866,0.86,0.886\n-0.766,0.351,0.805\n-0.67,1,0.374\n-1,1,0.956\n-0.651,0.094,0.36\n-0.946,0.949,0.999\n-0,0,0.006\n-0.103,0.238,0.105\n-0.85,0,0.694\n-0.004,0.02,0.02\n-0.98,0.85,0.082\n-0.365,0,0.42\n-0,0,0\n-1,0.781,1\n-0,0.002,0\n-0,0,0\n-1,1,0.668\n-0.635,0.213,0.416\n-0.888,0.894,0.772\n-0.074,0.044,0.034\n-0.641,0.949,0.27\n-0.896,0.079,0.394\n-0.907,0.827,0.873\n-1,0.799,1\n-0.977,0.637,1\n-0.782,0.392,0.811\n-0.978,0.949,0.953\n-0,0,0\n-0.018,0.116,0.028\n-0.95,0.692,0\n-0.004,0.019,0\n-1,0.977,0.969\n-0.962,0.795,0.889\n-0.072,0.284,0.128\n-0.989,0.816,0.913\n-0.103,0.062,0.049\n-0,0,0.008\n-0.967,0.764,0.039\n-0.514,0.359,0.319\n-0.041,0,0\n-1,0.957,0.69\n-0,0.004,0\n-1,1,1\n-1,0.887,0.01\n-0.04,0.171,0.006\n-1,1,1\n-1,1,0.979\n-1,1,1\n-0.904,0.889,0.986\n-0.939,0.823,0.952\n-0.131,0.509,0\n-0.995,0.949,1\n-0.979,0.794,0.915\n-1,1,1\n-0.824,0.847,0.869\n-0.04,0.029,0.022\n-0.83,0.85,0.922\n-1,0.997,1\n-0.989,0.46,0.867\n-0.066,0.171,0.008\n-0.176,0.154,0.092\n-0.008,0.028,0.295\n-0.942,0.887,0.918\n-0,0,0\n-0.431,0.325,0.019\n-0.003,0,0\n-0.833,0.627,0.823\n-0,0.015,0\n-1,1,1\n-0.173,0.03,0.07\n-0.721,0.749,0.583\n-0.111,0,0.21\n-0.997,0.994,1\n-0.611,0.316,0.418\n-0.126,0,0.031\n-0,0,0\n-1,1,1\n-1,0.879,0.885\n-0.004,0,0\n-0.099,0.003,0.007\n-0,0,0\n-0.727,0.028,0.519\n-0.879,0.943,0.691\n-0,0,0\n-0.673,0.796,0.565\n-0.924,0.885,0.979\n-1,0.92,0.907\n-0,0,0\n-0.868,0.646,0.51\n-0.048,0.009,0.022\n-0.041,0.007,0.002\n-0.687,0.113,0.424\n-0,0,0\n-0.893,0.597,0.856\n-0,0,0\n-0.976,0.822,1\n-0.076,0.011,0.002\n-0,0,0\n-0.847,0.93,0.929\n-0,0,0\n-0.531,0.224,0.329\n-0.987,0.762,0.934\n-0.12,0.376,0.196\n-1,0.88,0.754\n-0.943,0.899,0.94\n-0.892,0.804,0.813\n-0,0,0\n-0.907,0.766,0.904\n-0.814,0.889,0.534\n-0.015,0.024,0.045\n-1,0.997,0.882\n-0.418,0.177,0\n-1,0.982,1\n-0.125,0.172,0.159\n-1,1,1\n-0.349,0.235,0.024\n-0.999,0.958,1\n-0.998,0.487,0.491\n-1,0.986,0.795\n-1,1,0.768\n-0.879,0.41,0.542\n-0.108,0.053,0.223\n-1,1,1\n-0.965,0.865,0.96\n-0.007,0.014,0.036\n-0.055,0.09,0.036\n-0.639,0.915,0.915\n-0.043,0.007,0.008\n-0.912,0.576,0.857\n-0.046,0,0.086\n-0,0,0\n-0,0,0\n-0,0.016,0.016\n-0.023,0,0\n-0.165,0.165,0.109\n-0,0,0\n-0.128,0.159,0.096\n-0.017,0,0.023\n-0,0,0.067\n-0.098,0,0.114\n-0.028,0.044,0.092\n-0,0,0\n-0,0,0\n-0,0,0.003\n-0.139,0,0.129\n-0,0,0\n-0,0,0\n-0,0,0\n-0,0.001,0\n-0,0,0\n-0,0,0.328\n-0,0,0.103\n-0,0,0.003\n-0,0,0\n-0,0,0.337\n-0,0,0\n-0,0,0.046\n-0,0,0\n-0,0,0\n-0.04,0.058,0.014\n-0.004,0,0.086\n-0,0,0\n-0.134,0.165,0.091\n-0,0.004,0\n-0,0,0.04\n-0,0,0\n-0,0,0\n-0.077,0.091,0.104\n-0.131,0.085,0.249\n-0,0,0\n-0,0,0.025\n-0,0,0.057\n-0,0,0\n-0,0,0.025\n-0.05,0.04,0.087\n-0,0,0\n-0,0,0\n-0.024,0.024,0.016\n-0,0,0\n-0.056,0.531,0.028\n-0.983,1,0.54\n-0.04,0.626,0.456\n-0.498,0.01,0.942\n-0.002,0,0\n-0.01,1,0.988\n-0.983,0.026,0.376\n-0.491,0.587,0.51\n-0.957,0.951,0.477\n-0.118,0.43,0.434\n-0.041,0.401,0.972\n-0.942,0.944,0.07\n-0.273,0.007,1\n-0.936,0.439,0.55\n-0.066,0.469,0.099\n-0.043,0.452,0.034\n-0.075,0.487,0.922\n-0.895,0.944,0.519\n-0.48,0.635,0.998\n-0.044,0.029,0.458\n-0.972,0.068,0.573\n-0.958,0.018,0.013\n-0.097,0.975,0.638\n-0.166,0.062,0.065\n-0.019,0.004,0.468\n-0,0.455,0\n-1,0.327,1\n-1,1,1\n-1,0.92,0.487\n-1,0.464,0.548\n-0,0,0.473\n-1,1,1\n-0,0,0\n-0.645,0.508,1\n-1,1,1\n-1,0,0.46\n-0,0,1\n-0,1,0.488\n-1,1,0.353\n-0.362,0.466,0\n-0,0.609,0\n-1,1,0.487\n-1,1,0.64\n-1,0,0\n-1,0,1\n-0.515,1,1\n-0,0,0\n-0,0,1\n-0.013,1,1\n-1,0,0.006\n-0,0,0.446\n-0.693,0.882,0\n-0.438,0.529,0\n-0.484,0.126,0.462\n-0.034,0,0\n-1,1,1\n-0.024,0,0.567\n-0.428,0.638,0.345\n-0.828,0,0.458\n-0,1,0\n-0,0.706,0.487\n-0,1,0.498\n-0.876,0.525,0.539\n-0.719,0,0.548\n-0.838,0.476,0.459\n' |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 GEO/test-data/input.csv --- a/GEO/test-data/input.csv Tue Feb 28 05:11:54 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -ID,Phenotype -GSM1247787,melanoma -GSM1247784,melanoma -GSM1247733,healthy |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 GEO/tool_dependencies.xml --- a/GEO/tool_dependencies.xml Tue Feb 28 05:11:54 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,273 +0,0 @@\n-<?xml version="1.0"?>\n-<tool_dependency>\n- <install version="1.0">\n- <actions>\n- <action type="setup_r_environment">\n- <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">\n- <package name="R" version="3.2.1"/>\n- </repository>\n- <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49">\n- https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz\n- </package>\n- <package sha256sum="0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f">\n- https://depot.galaxyproject.org/software/labeling/labeling_0.3.tar.gz\n- </package>\n- <package sha256sum="762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881">\n- https://depot.galaxyproject.org/software/DO.db/DO.db_2.9.tar.gz\n- </package>\n- <package sha256sum="de6f46918b40bcf4f8c03442f2a0411f1796794e0e7b00770ed0aac56601833d">\n- https://bioarchive.galaxyproject.org/fgsea_1.1.2.tar.gz\n- </package>\n- <package sha256sum="7f1aa58085a030b7855a4e189bea2f17ff72333a1f884f0ab7f5af1fbe101397">\n- https://bioarchive.galaxyproject.org/GOSemSim_2.1.2.tar.gz\n- </package>\n- <package sha256sum="dc64ed09b8b5f8d66ed4936cde3491974d6bc5178dd259b6eab7ef3936aa5602">\n- https://depot.galaxyproject.org/software/igraph/igraph_1.0.1.tar.gz\n- </package>\n- <package sha256sum="f9e132c35d3af919cff291465d030817ff74e56eb6b2770390ae8566881b62ed">\n- https://bioarchive.galaxyproject.org/qvalue_2.7.0.tar.gz\n- </package>\n- <package sha256sum="6d3783610379be4c5676d9236cf66276a166b5b96c18f2759e9b219758959b6b">\n- https://depot.galaxyproject.org/software/reshape2/reshape2_1.4.2.tar.gz\n- </package>\n- <package sha256sum="642b88fb1fce7bac72a0038ce532b65b8a79dffe826fec25033cf386ab630cd3">\n- https://depot.galaxyproject.org/software/scales/scales_0.4.1.tar.gz\n- </package>\n- <package sha256sum="51a74de64296d7cbed04a015a9f9725de95adb5e04301d1cd58190d7365fb104">\n- https://bioarchive.galaxyproject.org/biomaRt_2.31.3.tar.gz\n- </package>\n- <package sha256sum="801e4869830ff3da1d38e41f5a2296a54fc10a7419c6ffb108582850c701e76f">\n- https://depot.galaxyproject.org/software/gtable/gtable_0.2.0.tar.gz\n- </package>\n- <package sha256sum="ed8a8bd0591223f742be80fd1cd8c4a9618d0f04011ec95c272b61ea45193104">\n- https://depot.galaxyproject.org/software/tibble/tibble_1.2.tar.gz\n- </package>\n- <package sha256sum="13738f55b2044184fe91f53d17516a445dfb508227527921218cda6f01f98dcb">\n- https://depot.galaxyproject.org/software/lazyeval/lazyeval_0.2.0.tar.gz\n- </package>\n- <package sha256sum="8097ec0e4868f6bf746f821cff7842f696e874bb3a84f1b2aa977ecd961c3e4e">\n- https://depot.galaxyproject.org/software/gdata/gdata_2.17.0.tar.gz\n- </package>\n- <package sha256sum="d32a73febf00930355cc00f3e4e71357412e0f163faae6a4bf7f552cacfe9af4">\n- https://depot.galaxyproject.org/software/caTools/caTools_1.17.1.tar.gz\n- </package>\n- <package sha256sum="1363645a9a128f6'..b' <package sha256sum="d89db98ea1025e38d59daeff965dd8174bbb94a961cb966a83760ac1a87a36b8">\n- https://depot.galaxyproject.org/software/reshape/reshape_0.8.6.tar.gz\n- </package>\n- <package sha256sum="d999620688354c283de5bb305203f5db70271b4dfdc23577cae8c2ba94c9e349">\n- https://depot.galaxyproject.org/software/quadprog/quadprog_1.5-5.tar.gz\n- </package>\n- <package sha256sum="cd26dbd60b2e2060541c4bb579ec1e0f6c262501431460b096b5fef323204432">\n- https://bioarchive.galaxyproject.org/GEOquery_2.41.0.tar.gz\n- </package>\n- <package sha256sum="bee70645c7cc88250761092762a9d293b4644f311047baecf49fde766d3059bc">\n- https://bioarchive.galaxyproject.org/Biobase_2.35.0.tar.gz\n- </package>\n- <package sha256sum="c6133611cc991dfc17410d06a9ddcc6dcff0153bceffdf7d5a9b7dc42f31afa6">\n- https://depot.galaxyproject.org/software/org.Hs.eg.db/org.Hs.eg.db_3.4.0.tar.gz\n- </package>\n- <package sha256sum="cf61732ef9b38ecb6579055d1cd145198ad23a5a9ae4378f94a1494e6c56c884">\n- https://depot.galaxyproject.org/software/data.table/data.table_1.10.0.tar.gz\n- </package>\n- <package sha256sum="d47be4430a1c343c20f9d3f67b8511506904e46be13ea4199769f012f1449209">\n- https://depot.galaxyproject.org/software/GO.db/GO.db_3.4.0.tar.gz\n- </package>\n- <package sha256sum="dfccd4b4d6ec90cd7628fd128d2456d792f406cee4d32b13448dcb0ffe4ab056">\n- https://depot.galaxyproject.org/software/NMF/NMF_0.20.6.tar.gz\n- </package>\n- <package sha256sum="7fa594d9576592e393283ec4fc79fd72128f663bd516e05651957ce1e6fe3c38">\n- https://depot.galaxyproject.org/software/colorspace/colorspace_1.3-1.tar.gz\n- </package>\n- <package sha256sum="31151eaf36f70bdc1172da5ff5088ee51cc0a3db4ead59c7c38c25316d580dd1">\n- https://depot.galaxyproject.org/software/dichromat/dichromat_2.0-0.tar.gz\n- </package>\n- <package sha256sum="7a4957c66ff622d7d1456adfbb728c60d406cdb2a754979797f9dcb0dc8fee99">\n- https://depot.galaxyproject.org/software/fastmatch/fastmatch_1.0-4.tar.gz\n- </package>\n- <package sha256sum="5183e8dd7943df11c0f44460566adf06c03d5320f142699298f516d423b06ce1">\n- https://depot.galaxyproject.org/software/irlba/irlba_2.1.2.tar.gz\n- </package>\n- <package sha256sum="19ad78c16bd5757333e7abbd5eebcec081deb494c9a4b6eec6919a3747b3386f">\n- https://depot.galaxyproject.org/software/pkgmaker/pkgmaker_0.22.tar.gz\n- </package>\n- <package sha256sum="58a5c43b8012ca5e509fa29a8daf6f24f097b8eb021a723f6a9c33db1dd3f430">\n- https://depot.galaxyproject.org/software/registry/registry_0.3.tar.gz\n- </package>\n- <package sha256sum="27019835b750f470b13dbb7fecd3b839a61b52774e23fffa191f919533768fb9">\n- https://depot.galaxyproject.org/software/rngtools/rngtools_1.2.4.tar.gz\n- </package>\n- <package sha256sum="605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f">\n- https://depot.galaxyproject.org/software/FDb.InfiniumMethylation.hg19/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz\n- </package>\n- </action>\n- </actions>\n- </install>\n- </tool_dependency>\n' |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 getGEO/.Rhistory --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGEO/.Rhistory Mon Mar 20 06:54:27 2017 -0400 |
| b |
| @@ -0,0 +1,7 @@ +??options +options(warn = -1) ++options("download.file.method"="wget") +options("download.file.method"="wget") +options(warn = -1,"download.file.method"="wget") +??getPlatform +??getPlatform |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 getGEO/._.DS_Store |
| b |
| Binary file getGEO/._.DS_Store has changed |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 getGEO/getGEO.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGEO/getGEO.R Mon Mar 20 06:54:27 2017 -0400 |
| [ |
| @@ -0,0 +1,54 @@ +require("BiocGenerics", quietly = TRUE) +require("data.table", quietly = TRUE) +require("GEOquery", quietly = TRUE) +require("rtracklayer", quietly = TRUE) +require("FDb.InfiniumMethylation.hg19", quietly = TRUE) + +options("download.file.method.GEOquery"="wget") +options(warn = -1) + +args <- commandArgs(trailingOnly = TRUE) +GSMTable = args[1] +protocol = args[2] +platform = args[3] +Data_Table = args[4] + +TAB = fread(GSMTable) + +if (is.null(TAB)) { + stop("Must specify input files") +} else { + GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE) + IlmnIDTable <- Table(GEODataTable) + MetaData <- data.frame(Meta(GEODataTable)) + + + write.table(MetaData, protocol, row.names = FALSE, sep = "\t") +} + +hm450.hg19 <- getPlatform() + +IlmnInfo <- + data.table( + IlmnID = names(hm450.hg19), + CHR = as.data.frame(hm450.hg19@seqnames)$value, + BP = as.numeric(hm450.hg19@elementMetadata$probeStart) + ) + + +write.table(IlmnInfo, platform, row.names = FALSE, sep = "\t") + + +if (length(TAB$ID) > 1) { + mysamples <- + do.call("data.table", lapply(TAB$ID[-1], function(x) + Table(getGEO(x, getGPL = FALSE))[, -1])) + + gmSet <- data.table(IlmnIDTable[, -1], mysamples) + +} else { + gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE)) +} + +write.table(gmSet, Data_Table, row.names = FALSE,quote=FALSE,sep="\t") + |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 getGEO/getGEO.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGEO/getGEO.xml Mon Mar 20 06:54:27 2017 -0400 |
| [ |
| @@ -0,0 +1,39 @@ +<tool id="GEO" name="getGEO" version="1.16.2"> + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + </requirements> +<stdio> + <exit_code range="1:" /> + </stdio> + <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$protocol" "$platform" "$Data_Table"</command> + <inputs> + <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable"> + <validator type="empty_field" message="This field is required."/> + </param> + </inputs> + <outputs> + <data format="txt" name="protocol" label="protocol.txt"/> + <data format="txt" name="platform" label="platform.txt"/> + <data format="txt" name="Data_Table" label="Data_Table.txt"/> + </outputs> + <tests> + <test> + <param name="test"> + <element name="test-data"> + <collection type="data"> + <element name="GSMTable" value="test-data/input.csv" /> + </collection> + </element> + </param> + <output format="txt" name="protocol" label="test-data/protocol.txt"/> + <output format="txt" name="platform" label="test-data/platform.txt"/> + <output format="txt" name="Data_Table" label="test-data/Data_Table.txt"/> + </test> + </tests> + <help> +**Description** +</help> +<citations> +GEO +</citations> +</tool> |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 getGEO/test-data/._.DS_Store |
| b |
| Binary file getGEO/test-data/._.DS_Store has changed |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 getGEO/test-data/._input.csv |
| b |
| Binary file getGEO/test-data/._input.csv has changed |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 getGEO/test-data/IlmnTable.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGEO/test-data/IlmnTable.txt Mon Mar 20 06:54:27 2017 -0400 |
| b |
| b'@@ -0,0 +1,485578 @@\n+"IlmnID","CHR","BP"\n+"cg04913815","chr16",60438\n+"cg01686861","chr16",60700\n+"cg05558259","chr16",61037\n+"cg26978960","chr16",62412\n+"cg03792876","chr16",73195\n+"cg09699726","chr16",91554\n+"cg07549526","chr16",91663\n+"cg02851049","chr16",101212\n+"cg11876012","chr16",101638\n+"cg14820573","chr16",102073\n+"cg14747225","chr16",102976\n+"cg16670573","chr16",103375\n+"cg09499248","chr16",103483\n+"cg00762468","chr16",103568\n+"cg05055400","chr16",103592\n+"cg09969830","chr16",103646\n+"cg00958578","chr16",103715\n+"cg11653271","chr16",103723\n+"cg01188584","chr16",103853\n+"cg03974483","chr16",103985\n+"cg08718695","chr16",104135\n+"cg01062126","chr16",104539\n+"cg00992207","chr16",107404\n+"cg00914902","chr16",108066\n+"cg27248189","chr16",110257\n+"cg06194960","chr16",111362\n+"cg07608562","chr16",111610\n+"cg20220196","chr16",111753\n+"cg09201525","chr16",111823\n+"cg03333116","chr16",112396\n+"cg04721268","chr16",112802\n+"cg01403103","chr16",112804\n+"cg01502407","chr16",113107\n+"cg04322210","chr16",114987\n+"cg26933686","chr16",115957\n+"cg00179196","chr16",117934\n+"cg07405083","chr16",119384\n+"cg06934747","chr16",120902\n+"cg00525011","chr16",122031\n+"cg03948744","chr16",122515\n+"cg00079891","chr16",122716\n+"cg09113560","chr16",122764\n+"cg04995976","chr16",123198\n+"cg06230303","chr16",123353\n+"cg01262217","chr16",123363\n+"cg04260507","chr16",123553\n+"cg17199481","chr16",123676\n+"cg01422009","chr16",125896\n+"cg03462322","chr16",126397\n+"cg16383109","chr16",126403\n+"cg03110993","chr16",126800\n+"cg03492469","chr16",126855\n+"cg05501742","chr16",126844\n+"cg16003913","chr16",127072\n+"cg04257263","chr16",127088\n+"cg15017278","chr16",127401\n+"cg02729269","chr16",127772\n+"cg07395378","chr16",127904\n+"cg01609171","chr16",127949\n+"cg10009236","chr16",127968\n+"cg05397937","chr16",128446\n+"cg15768556","chr16",128630\n+"cg05394456","chr16",129230\n+"cg10143220","chr16",129454\n+"cg00935108","chr16",129562\n+"cg02949481","chr16",131514\n+"cg05791870","chr16",136656\n+"cg07484220","chr16",136761\n+"cg07405534","chr16",139691\n+"cg26925590","chr16",139704\n+"cg07371452","chr16",139732\n+"cg04807152","chr16",147558\n+"cg16730559","chr16",157323\n+"cg02353723","chr16",163133\n+"cg09430181","chr16",175615\n+"cg02028423","chr16",185078\n+"cg01527023","chr16",188138\n+"cg00928894","chr16",188221\n+"cg02369618","chr16",188603\n+"cg09580244","chr16",188684\n+"cg02783232","chr16",188741\n+"cg08524197","chr16",188802\n+"cg02855078","chr16",188815\n+"cg08969593","chr16",188855\n+"cg06171619","chr16",188884\n+"cg00389577","chr16",189052\n+"cg24399405","chr16",189577\n+"cg27009501","chr16",192791\n+"cg06929449","chr16",199366\n+"cg10317591","chr16",199773\n+"cg08957279","chr16",202263\n+"cg10164238","chr16",202320\n+"cg21960110","chr16",202434\n+"cg01839639","chr16",202542\n+"cg25425005","chr16",202905\n+"cg07263153","chr16",202926\n+"cg08400316","chr16",204221\n+"cg02279719","chr16",204474\n+"cg06459847","chr16",204601\n+"cg07498624","chr16",204783\n+"cg01923692","chr16",204949\n+"cg06031493","chr16",210205\n+"cg05390075","chr16",210528\n+"cg07067950","chr16",212416\n+"cg07893512","chr16",214728\n+"cg05057452","chr16",214922\n+"cg25322095","chr16",215002\n+"cg07466193","chr16",215362\n+"cg01744019","chr16",215545\n+"cg09812623","chr16",215733\n+"cg08393070","chr16",215743\n+"cg01558909","chr16",215797\n+"cg26540367","chr16",215816\n+"cg06319822","chr16",215912\n+"cg26976732","chr16",216052\n+"cg21664030","chr16",216244\n+"cg04141813","chr16",216450\n+"cg03309232","chr16",216626\n+"cg12251336","chr16",216719\n+"cg09523819","chr16",216709\n+"cg04321267","chr16",219107\n+"cg04377849","chr16",221536\n+"cg26637826","chr16",221542\n+"cg04938149","chr16",221811\n+"cg15597257","chr16",222837\n+"cg00697413","chr16",222858\n+"cg16263182","chr16",223351\n+"cg05956679","chr16",223360\n+"cg01319583","chr16",224880\n+"cg01704105","chr16",225666\n+"cg08923033","chr16",226002\n+"cg06235582","chr16",226668\n+"cg27452732","chr16",226670\n+"cg10647513","chr16",227155\n+"cg09434193","chr16",227185\n+"cg08923355","chr16",227469\n+"cg05933901","chr16'..b'16637094\n+"cg09804407","chrY",16733251\n+"cg08816194","chrY",16733442\n+"cg07795413","chrY",16733930\n+"cg01073572","chrY",16924422\n+"cg01498999","chrY",16939335\n+"cg03278611","chrY",16941543\n+"cg09300505","chrY",16942106\n+"cg05939513","chrY",16942232\n+"cg02340092","chrY",16945913\n+"cg25667057","chrY",17567474\n+"cg23834181","chrY",17567486\n+"cg03672679","chrY",17567897\n+"cg04792227","chrY",17568097\n+"cg00679624","chrY",17568445\n+"cg20764275","chrY",17568616\n+"cg14742615","chrY",17569363\n+"cg01882666","chrY",17571429\n+"cg03905640","chrY",19625260\n+"cg01209756","chrY",19671414\n+"cg17115812","chrY",19678480\n+"cg14151065","chrY",19678487\n+"cg25012987","chrY",19691491\n+"cg16292375","chrY",19691502\n+"cg16894943","chrY",20488221\n+"cg06060201","chrY",20488232\n+"cg04170994","chrY",20488245\n+"cg09408193","chrY",20501241\n+"cg10252249","chrY",20508275\n+"cg23308414","chrY",20508314\n+"cg26046487","chrY",20736099\n+"cg10646950","chrY",20748734\n+"cg00479827","chrY",21036938\n+"cg10691859","chrY",21041339\n+"cg15281205","chrY",21100424\n+"cg05230942","chrY",21155222\n+"cg13765957","chrY",21208573\n+"cg26251715","chrY",21236181\n+"cg03244189","chrY",21238424\n+"cg13845521","chrY",21238886\n+"cg10811597","chrY",21239219\n+"cg11816202","chrY",21239284\n+"cg00212031","chrY",21239300\n+"cg15345074","chrY",21239413\n+"cg11684211","chrY",21239559\n+"cg06628792","chrY",21240004\n+"cg00121626","chrY",21664248\n+"cg15027426","chrY",21664556\n+"cg00876332","chrY",21664717\n+"cg15794778","chrY",21664973\n+"cg09228985","chrY",21666030\n+"cg06065495","chrY",21666261\n+"cg03533500","chrY",21668372\n+"cg06231362","chrY",21726406\n+"cg25756647","chrY",21728575\n+"cg06502680","chrY",21728904\n+"cg20864678","chrY",21728989\n+"cg14492024","chrY",21729001\n+"cg05725925","chrY",21729010\n+"cg05621349","chrY",21729021\n+"cg10076560","chrY",21729144\n+"cg15682993","chrY",21729203\n+"cg07731488","chrY",21729314\n+"cg05672930","chrY",21729555\n+"cg17660627","chrY",21729665\n+"cg14931215","chrY",21867654\n+"cg00308367","chrY",21868484\n+"cg27509967","chrY",21877683\n+"cg15329860","chrY",21906636\n+"cg25815185","chrY",21906868\n+"cg27049643","chrY",21906893\n+"cg26517491","chrY",21906895\n+"cg15662272","chrY",21906974\n+"cg02522936","chrY",22680010\n+"cg10799208","chrY",22681388\n+"cg26928789","chrY",22682345\n+"cg09081202","chrY",22735272\n+"cg01988452","chrY",22736480\n+"cg13308744","chrY",22736536\n+"cg10172760","chrY",22736785\n+"cg10620659","chrY",22737343\n+"cg15422579","chrY",22737376\n+"cg15059553","chrY",22737505\n+"cg01644972","chrY",22737508\n+"cg02233190","chrY",22737591\n+"cg26983535","chrY",22737594\n+"cg11225091","chrY",22737615\n+"cg03750315","chrY",22737848\n+"cg02884332","chrY",22737946\n+"cg08715207","chrY",22737921\n+"cg08820785","chrY",22738029\n+"cg10593480","chrY",22738723\n+"cg00063477","chrY",22741795\n+"cg01900066","chrY",22754881\n+"cg07747963","chrY",22917039\n+"cg10841270","chrY",22917104\n+"cg01943289","chrY",22917296\n+"cg17741448","chrY",22917782\n+"cg02012379","chrY",22917846\n+"cg00676506","chrY",22917913\n+"cg06322277","chrY",22917937\n+"cg26058907","chrY",22917894\n+"cg02050847","chrY",22918038\n+"cg14029254","chrY",22918213\n+"cg02352633","chrY",23561638\n+"cg03416979","chrY",23566240\n+"cg05051262","chrY",23566524\n+"cg25427172","chrY",23566730\n+"cg10666546","chrY",23566863\n+"cg25640065","chrY",23569324\n+"cg16552926","chrY",23694843\n+"cg25918849","chrY",23753284\n+"cg11021362","chrY",23756676\n+"cg14467015","chrY",23757241\n+"cg15516537","chrY",24036834\n+"cg05999368","chrY",24044030\n+"cg15462332","chrY",24052484\n+"cg26497631","chrY",24331310\n+"cg06865724","chrY",24445690\n+"cg25914522","chrY",24452543\n+"cg13808036","chrY",24453658\n+"cg10267609","chrY",24453709\n+"cg00335297","chrY",24454479\n+"cg03827298","chrY",24454879\n+"cg26983430","chrY",24549675\n+"cg22051787","chrY",24549677\n+"cg01757887","chrY",25114762\n+"cg00061679","chrY",25314123\n+"cg03930849","chrY",26716241\n+"cg17939569","chrY",27009430\n+"cg13365400","chrY",27210334\n+"cg21106100","chrY",28555488\n+"cg08265308","chrY",28555502\n+"cg14273923","chrY",28555912\n' |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 getGEO/test-data/MetaTable.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGEO/test-data/MetaTable.txt Mon Mar 20 06:54:27 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +"channel_count","characteristics_ch1","contact_address","contact_city","contact_country","contact_department","contact_institute","contact_name","contact_zip.postal_code","data_processing","data_row_count","description","extract_protocol_ch1","geo_accession","hyb_protocol","label_ch1","label_protocol_ch1","last_update_date","molecule_ch1","organism_ch1","platform_id","scan_protocol","series_id","source_name_ch1","status","submission_date","supplementary_file","taxid_ch1","title","type" +"1","sample type: melanoma cell line","Barngatan 2B","Lund","Sweden","Dept of Oncology","Lund University","Martin,,Lauss","22185","Raw intensities for methylated (M) and unmethylated (U) signal were extracted from Illumina’s GenomeStudio. Beta-values were calculated as M/(M+U). A total of 496 missing values (melanomas) were imputed using k-nearest neighbor imputation (k=10). For each sample we performed a peak-based correction of Illumina I and II chemical assays. For both assays we smoothed the beta values (Epanechnikov smoothing kernel) to estimate unmethylated and methylated peaks, respectively; and the unmethylated peak was moved to 0 and the methylated peak to 1 using linear scaling, with beta-values in between stretched accordingly. Beta-values below 0 were set back to 0 and values above 1 were set to 1.","485577","melanoma cell line","Genomic DNA was extracted from the biopsies using QIAamp DNA Mini Kit (Qiagen). A total of 500 ng of DNA were used for bisulfite treatment, using the EZ DNA Methylation Kit (Zymo). We hybridized 200 ng in 4 μl to the Infinium Human Methylation450 BeadChip array.","GSM1247787","Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol","Cy5 and Cy3","Standard Illumina Protocol","May 17 2015","genomic DNA","Homo sapiens","GPL13534","Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting","GSE51547","SKMEL3","Public on May 17 2015","Oct 22 2013","NONE","9606","genomic DNA from Sample SKMEL3","genomic" |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 getGEO/test-data/gmTable.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGEO/test-data/gmTable.txt Mon Mar 20 06:54:27 2017 -0400 |
| b |
| b'@@ -0,0 +1,485578 @@\n+"V1","V1","V2"\n+0.509,0.716,0.395\n+0.647,0.561,0.372\n+0.83,0.52,0.559\n+0.618,0.698,0.573\n+0.37,0.216,0.522\n+0.464,0.219,0.62\n+0.421,0.607,0.639\n+0.425,0.379,0.602\n+0,0,0\n+0.555,0.559,0.611\n+0.327,0.357,0.387\n+0.8,0.683,0.398\n+0.418,0.154,0.614\n+0.538,0.469,0.409\n+0.312,0.167,0.473\n+0.261,0.351,0.584\n+0.591,0.622,0.521\n+0.52,0.469,0.639\n+0.595,1,0.639\n+0.535,0.774,0.403\n+0.342,0.387,0.502\n+0.801,0.72,0.726\n+0.581,0.748,0.867\n+0.445,0.567,0.553\n+0.699,0.532,0.498\n+0.446,0.411,0.335\n+0.62,0.363,0.37\n+0.82,0.368,0.717\n+0.997,0,0.58\n+0.355,0.447,0.543\n+0.443,0.434,0.574\n+0.004,0,0.007\n+0.482,0.427,0.663\n+0.841,0.94,0.615\n+0.76,0.624,0.878\n+0.787,0.847,0.511\n+0.887,0.893,0.789\n+0.553,0.521,0.607\n+0.468,0.502,0.387\n+0.693,0.609,0.403\n+0.545,0.643,0.623\n+0.765,0.567,0.202\n+0.438,0.334,0.362\n+0.612,0.625,0.627\n+0.735,0.651,0.699\n+0.747,0.441,0.666\n+0.536,0.536,0.429\n+0.22,0.184,0.543\n+0.538,0.297,0.289\n+0.403,0.74,0.725\n+0.484,0.495,0.369\n+0.223,0.172,0.323\n+0.486,0.436,0.416\n+0.49,0.273,0.557\n+0.691,0.62,0.311\n+0.192,0.437,0.469\n+0.536,0.242,0.585\n+0.357,0.464,0.573\n+0.465,0.497,0.441\n+0.615,0.336,0.466\n+0,1,0.504\n+0.044,0.001,0.074\n+0.242,0.232,0.39\n+0.862,0.789,0.598\n+0.761,0.014,0.614\n+0.332,0.545,0.567\n+0.532,0.47,0.31\n+0.486,0.293,0.493\n+0.235,0.21,0.348\n+0,0,0.011\n+0,0,0\n+0.858,0.531,0.504\n+0.584,0.531,0.532\n+0.255,0.223,0.426\n+0.37,0.451,0.581\n+0.404,0.321,0.39\n+0.154,0.072,0.151\n+0.696,0.646,0.591\n+0.354,0.235,0.708\n+0.598,0.242,0.62\n+0.321,0.494,0.507\n+0.316,0.292,0.395\n+0.722,0.577,0.616\n+0.289,0.075,0.4\n+0.316,0.529,0.536\n+0.523,0.608,0.429\n+0.552,0.302,0.244\n+1,0.032,0.401\n+0.587,1,0.261\n+0.201,0.177,0.173\n+0.459,0.388,0.387\n+0.219,0.611,0.739\n+0.395,0.638,0.593\n+0.4,0.225,0.681\n+0.271,0.406,0.339\n+0.361,0.251,0.434\n+1,0,0.643\n+0.922,0.489,0.496\n+0.431,0.592,0.608\n+0.677,0.335,0.557\n+0.235,0.213,0.391\n+0.446,0.109,0.39\n+0.474,0.394,0.326\n+1,0,0.409\n+0.415,0.553,0.569\n+0.476,0.685,0.669\n+0.538,0.913,0.36\n+0.531,0.489,0.568\n+0.278,0.313,0.441\n+0.303,0.381,0.589\n+0.366,0.594,0.711\n+0.908,0.754,0.667\n+0,0,0.049\n+0.474,0.607,0.469\n+0.704,0.725,0.601\n+0.857,0.494,0.675\n+0.395,0.571,0.62\n+0.877,0.739,0.484\n+0.687,0.458,0.486\n+0.538,0.308,0.39\n+0.269,0.295,0.508\n+0.343,0.222,0.327\n+1,0.139,0.807\n+0.946,0.005,0.716\n+0.328,0.321,0.362\n+0.516,0.453,0.53\n+0.273,0.153,0.492\n+0.284,0.192,0.293\n+0.284,0.429,0.719\n+0.628,0.748,0.405\n+0.307,0.364,0.282\n+0.404,0.521,0.561\n+0.492,0.776,0.56\n+0.445,0.554,0.382\n+0.395,0.523,0.479\n+0.335,0.594,0.775\n+0.77,0.051,0.359\n+0.53,0.286,0.712\n+0.595,0.776,0.513\n+0.638,0.743,0.691\n+0.181,0.158,0.477\n+0.673,0.522,0.39\n+0.987,0.058,0.463\n+0.502,0.251,0.403\n+0.423,0.63,0.597\n+0.311,0.376,0.348\n+0.693,0.424,0.398\n+0.664,0.545,0.465\n+0.539,0.303,0.403\n+0.537,0.443,0.467\n+0.577,0.414,0.518\n+0.488,0.395,0.234\n+0.531,0.396,0.394\n+0.437,0.399,0.353\n+0.438,0.567,0.391\n+0.261,0.235,0.504\n+0.365,0.466,0.333\n+0.661,0.238,0.449\n+0.696,0.71,0.464\n+0.348,0.327,0.371\n+0.035,0.08,0.551\n+0.368,0.3,0.497\n+0.696,0.577,0.532\n+0.618,0.362,0.536\n+0.634,0.791,0.525\n+0.614,0.309,0.54\n+0.357,0.411,0.464\n+0.346,0.198,0.619\n+0.518,0.42,0.384\n+0.274,0.525,0.643\n+0.447,0.371,0.376\n+0.313,0.579,0.429\n+0.327,0.299,0.458\n+0.458,0.396,0.426\n+0.541,0.475,0.464\n+0.457,0.461,0.77\n+0.439,0.497,0.523\n+0.674,0.436,0.635\n+0.223,0.159,0.643\n+0.639,0.507,0.563\n+0.719,0.559,0.421\n+0.543,0.399,0.306\n+1,0.462,0.73\n+0.382,0.625,0.536\n+0.513,0.311,0.479\n+0.37,0.387,0.383\n+0.485,0.439,0.319\n+0.434,0.348,0.515\n+0.418,0.551,0.464\n+0.369,0.42,0.619\n+0.853,0.504,0.842\n+0.623,0.526,0.356\n+0.446,0.475,0.384\n+0.507,0.479,0.324\n+0.496,0.685,0.649\n+0.363,0.238,0.409\n+0.719,0.299,0.547\n+0.273,0.447,0.639\n+0.112,0.16,0.071\n+0.497,0.358,0.59\n+0.527,0.571,0.453\n+0.342,0.19,0.38\n+0.864,0.674,0.83\n+0.588,0.311,0.707\n+0.439,0.374,0.47\n+0.489,0.55,0.496\n+0.393,0.247,0.322\n+0.357,0.284,0.42\n+0.366,0.266,0.692\n+0.409,0.483,0.519\n+0.685,0.749,0.997\n+0.381,0.498,0.464\n+0.689,1,0.711\n+0.436,0.173,0.683\n+0.835,0.893,0.894\n+0.795,0.704,0.438\n+0.326,0.86'..b'0.506\n+0.031,0.006,0\n+0.458,0.043,0.127\n+0.948,0.914,0.945\n+0.015,0.018,0.012\n+1,1,0.851\n+0.734,0.536,0.645\n+0.961,0.961,0.556\n+0.027,0.026,0.003\n+0.817,0.54,0.802\n+0.981,0.963,1\n+0.65,0.599,0.856\n+0.144,0.195,0.138\n+0,0,0\n+0.023,0,0.006\n+0,0.067,0.003\n+0.984,0.868,0.901\n+0.084,0.074,0.428\n+0.952,0.838,1\n+0.025,0,0.036\n+0.002,0.315,0\n+0.236,0,0.295\n+0.29,0.125,0.446\n+0.677,0.452,0.004\n+0,0,0\n+0.002,0,0\n+0,0,0\n+0.974,0.873,0.877\n+0.903,0.572,0.654\n+0.295,0.095,0.096\n+0.906,0.795,0.64\n+0.035,0.019,0.015\n+1,0.52,0.705\n+0.929,0.874,0.67\n+0.699,0.126,0.684\n+0.992,0.961,0.608\n+0.866,0.86,0.886\n+0.766,0.351,0.805\n+0.67,1,0.374\n+1,1,0.956\n+0.651,0.094,0.36\n+0.946,0.949,0.999\n+0,0,0.006\n+0.103,0.238,0.105\n+0.85,0,0.694\n+0.004,0.02,0.02\n+0.98,0.85,0.082\n+0.365,0,0.42\n+0,0,0\n+1,0.781,1\n+0,0.002,0\n+0,0,0\n+1,1,0.668\n+0.635,0.213,0.416\n+0.888,0.894,0.772\n+0.074,0.044,0.034\n+0.641,0.949,0.27\n+0.896,0.079,0.394\n+0.907,0.827,0.873\n+1,0.799,1\n+0.977,0.637,1\n+0.782,0.392,0.811\n+0.978,0.949,0.953\n+0,0,0\n+0.018,0.116,0.028\n+0.95,0.692,0\n+0.004,0.019,0\n+1,0.977,0.969\n+0.962,0.795,0.889\n+0.072,0.284,0.128\n+0.989,0.816,0.913\n+0.103,0.062,0.049\n+0,0,0.008\n+0.967,0.764,0.039\n+0.514,0.359,0.319\n+0.041,0,0\n+1,0.957,0.69\n+0,0.004,0\n+1,1,1\n+1,0.887,0.01\n+0.04,0.171,0.006\n+1,1,1\n+1,1,0.979\n+1,1,1\n+0.904,0.889,0.986\n+0.939,0.823,0.952\n+0.131,0.509,0\n+0.995,0.949,1\n+0.979,0.794,0.915\n+1,1,1\n+0.824,0.847,0.869\n+0.04,0.029,0.022\n+0.83,0.85,0.922\n+1,0.997,1\n+0.989,0.46,0.867\n+0.066,0.171,0.008\n+0.176,0.154,0.092\n+0.008,0.028,0.295\n+0.942,0.887,0.918\n+0,0,0\n+0.431,0.325,0.019\n+0.003,0,0\n+0.833,0.627,0.823\n+0,0.015,0\n+1,1,1\n+0.173,0.03,0.07\n+0.721,0.749,0.583\n+0.111,0,0.21\n+0.997,0.994,1\n+0.611,0.316,0.418\n+0.126,0,0.031\n+0,0,0\n+1,1,1\n+1,0.879,0.885\n+0.004,0,0\n+0.099,0.003,0.007\n+0,0,0\n+0.727,0.028,0.519\n+0.879,0.943,0.691\n+0,0,0\n+0.673,0.796,0.565\n+0.924,0.885,0.979\n+1,0.92,0.907\n+0,0,0\n+0.868,0.646,0.51\n+0.048,0.009,0.022\n+0.041,0.007,0.002\n+0.687,0.113,0.424\n+0,0,0\n+0.893,0.597,0.856\n+0,0,0\n+0.976,0.822,1\n+0.076,0.011,0.002\n+0,0,0\n+0.847,0.93,0.929\n+0,0,0\n+0.531,0.224,0.329\n+0.987,0.762,0.934\n+0.12,0.376,0.196\n+1,0.88,0.754\n+0.943,0.899,0.94\n+0.892,0.804,0.813\n+0,0,0\n+0.907,0.766,0.904\n+0.814,0.889,0.534\n+0.015,0.024,0.045\n+1,0.997,0.882\n+0.418,0.177,0\n+1,0.982,1\n+0.125,0.172,0.159\n+1,1,1\n+0.349,0.235,0.024\n+0.999,0.958,1\n+0.998,0.487,0.491\n+1,0.986,0.795\n+1,1,0.768\n+0.879,0.41,0.542\n+0.108,0.053,0.223\n+1,1,1\n+0.965,0.865,0.96\n+0.007,0.014,0.036\n+0.055,0.09,0.036\n+0.639,0.915,0.915\n+0.043,0.007,0.008\n+0.912,0.576,0.857\n+0.046,0,0.086\n+0,0,0\n+0,0,0\n+0,0.016,0.016\n+0.023,0,0\n+0.165,0.165,0.109\n+0,0,0\n+0.128,0.159,0.096\n+0.017,0,0.023\n+0,0,0.067\n+0.098,0,0.114\n+0.028,0.044,0.092\n+0,0,0\n+0,0,0\n+0,0,0.003\n+0.139,0,0.129\n+0,0,0\n+0,0,0\n+0,0,0\n+0,0.001,0\n+0,0,0\n+0,0,0.328\n+0,0,0.103\n+0,0,0.003\n+0,0,0\n+0,0,0.337\n+0,0,0\n+0,0,0.046\n+0,0,0\n+0,0,0\n+0.04,0.058,0.014\n+0.004,0,0.086\n+0,0,0\n+0.134,0.165,0.091\n+0,0.004,0\n+0,0,0.04\n+0,0,0\n+0,0,0\n+0.077,0.091,0.104\n+0.131,0.085,0.249\n+0,0,0\n+0,0,0.025\n+0,0,0.057\n+0,0,0\n+0,0,0.025\n+0.05,0.04,0.087\n+0,0,0\n+0,0,0\n+0.024,0.024,0.016\n+0,0,0\n+0.056,0.531,0.028\n+0.983,1,0.54\n+0.04,0.626,0.456\n+0.498,0.01,0.942\n+0.002,0,0\n+0.01,1,0.988\n+0.983,0.026,0.376\n+0.491,0.587,0.51\n+0.957,0.951,0.477\n+0.118,0.43,0.434\n+0.041,0.401,0.972\n+0.942,0.944,0.07\n+0.273,0.007,1\n+0.936,0.439,0.55\n+0.066,0.469,0.099\n+0.043,0.452,0.034\n+0.075,0.487,0.922\n+0.895,0.944,0.519\n+0.48,0.635,0.998\n+0.044,0.029,0.458\n+0.972,0.068,0.573\n+0.958,0.018,0.013\n+0.097,0.975,0.638\n+0.166,0.062,0.065\n+0.019,0.004,0.468\n+0,0.455,0\n+1,0.327,1\n+1,1,1\n+1,0.92,0.487\n+1,0.464,0.548\n+0,0,0.473\n+1,1,1\n+0,0,0\n+0.645,0.508,1\n+1,1,1\n+1,0,0.46\n+0,0,1\n+0,1,0.488\n+1,1,0.353\n+0.362,0.466,0\n+0,0.609,0\n+1,1,0.487\n+1,1,0.64\n+1,0,0\n+1,0,1\n+0.515,1,1\n+0,0,0\n+0,0,1\n+0.013,1,1\n+1,0,0.006\n+0,0,0.446\n+0.693,0.882,0\n+0.438,0.529,0\n+0.484,0.126,0.462\n+0.034,0,0\n+1,1,1\n+0.024,0,0.567\n+0.428,0.638,0.345\n+0.828,0,0.458\n+0,1,0\n+0,0.706,0.487\n+0,1,0.498\n+0.876,0.525,0.539\n+0.719,0,0.548\n+0.838,0.476,0.459\n' |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 getGEO/test-data/input.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGEO/test-data/input.csv Mon Mar 20 06:54:27 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +ID,Phenotype +GSM1247787,melanoma +GSM1247784,melanoma +GSM1247733,healthy |
| b |
| diff -r 19ea355e26b3 -r cbc8174bd361 getGEO/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGEO/tool_dependencies.xml Mon Mar 20 06:54:27 2017 -0400 |
| b |
| b'@@ -0,0 +1,273 @@\n+<?xml version="1.0"?>\n+<tool_dependency>\n+ <install version="1.0">\n+ <actions>\n+ <action type="setup_r_environment">\n+ <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">\n+ <package name="R" version="3.2.1"/>\n+ </repository>\n+ <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49">\n+ https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz\n+ </package>\n+ <package sha256sum="0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f">\n+ https://depot.galaxyproject.org/software/labeling/labeling_0.3.tar.gz\n+ </package>\n+ <package sha256sum="762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881">\n+ https://depot.galaxyproject.org/software/DO.db/DO.db_2.9.tar.gz\n+ </package>\n+ <package sha256sum="de6f46918b40bcf4f8c03442f2a0411f1796794e0e7b00770ed0aac56601833d">\n+ https://bioarchive.galaxyproject.org/fgsea_1.1.2.tar.gz\n+ </package>\n+ <package sha256sum="7f1aa58085a030b7855a4e189bea2f17ff72333a1f884f0ab7f5af1fbe101397">\n+ https://bioarchive.galaxyproject.org/GOSemSim_2.1.2.tar.gz\n+ </package>\n+ <package sha256sum="dc64ed09b8b5f8d66ed4936cde3491974d6bc5178dd259b6eab7ef3936aa5602">\n+ https://depot.galaxyproject.org/software/igraph/igraph_1.0.1.tar.gz\n+ </package>\n+ <package sha256sum="f9e132c35d3af919cff291465d030817ff74e56eb6b2770390ae8566881b62ed">\n+ https://bioarchive.galaxyproject.org/qvalue_2.7.0.tar.gz\n+ </package>\n+ <package sha256sum="6d3783610379be4c5676d9236cf66276a166b5b96c18f2759e9b219758959b6b">\n+ https://depot.galaxyproject.org/software/reshape2/reshape2_1.4.2.tar.gz\n+ </package>\n+ <package sha256sum="642b88fb1fce7bac72a0038ce532b65b8a79dffe826fec25033cf386ab630cd3">\n+ https://depot.galaxyproject.org/software/scales/scales_0.4.1.tar.gz\n+ </package>\n+ <package sha256sum="51a74de64296d7cbed04a015a9f9725de95adb5e04301d1cd58190d7365fb104">\n+ https://bioarchive.galaxyproject.org/biomaRt_2.31.3.tar.gz\n+ </package>\n+ <package sha256sum="801e4869830ff3da1d38e41f5a2296a54fc10a7419c6ffb108582850c701e76f">\n+ https://depot.galaxyproject.org/software/gtable/gtable_0.2.0.tar.gz\n+ </package>\n+ <package sha256sum="ed8a8bd0591223f742be80fd1cd8c4a9618d0f04011ec95c272b61ea45193104">\n+ https://depot.galaxyproject.org/software/tibble/tibble_1.2.tar.gz\n+ </package>\n+ <package sha256sum="13738f55b2044184fe91f53d17516a445dfb508227527921218cda6f01f98dcb">\n+ https://depot.galaxyproject.org/software/lazyeval/lazyeval_0.2.0.tar.gz\n+ </package>\n+ <package sha256sum="8097ec0e4868f6bf746f821cff7842f696e874bb3a84f1b2aa977ecd961c3e4e">\n+ https://depot.galaxyproject.org/software/gdata/gdata_2.17.0.tar.gz\n+ </package>\n+ <package sha256sum="d32a73febf00930355cc00f3e4e71357412e0f163faae6a4bf7f552cacfe9af4">\n+ https://depot.galaxyproject.org/software/caTools/caTools_1.17.1.tar.gz\n+ </package>\n+ <package sha256sum="1363645a9a128f6'..b' <package sha256sum="d89db98ea1025e38d59daeff965dd8174bbb94a961cb966a83760ac1a87a36b8">\n+ https://depot.galaxyproject.org/software/reshape/reshape_0.8.6.tar.gz\n+ </package>\n+ <package sha256sum="d999620688354c283de5bb305203f5db70271b4dfdc23577cae8c2ba94c9e349">\n+ https://depot.galaxyproject.org/software/quadprog/quadprog_1.5-5.tar.gz\n+ </package>\n+ <package sha256sum="cd26dbd60b2e2060541c4bb579ec1e0f6c262501431460b096b5fef323204432">\n+ https://bioarchive.galaxyproject.org/GEOquery_2.41.0.tar.gz\n+ </package>\n+ <package sha256sum="bee70645c7cc88250761092762a9d293b4644f311047baecf49fde766d3059bc">\n+ https://bioarchive.galaxyproject.org/Biobase_2.35.0.tar.gz\n+ </package>\n+ <package sha256sum="c6133611cc991dfc17410d06a9ddcc6dcff0153bceffdf7d5a9b7dc42f31afa6">\n+ https://depot.galaxyproject.org/software/org.Hs.eg.db/org.Hs.eg.db_3.4.0.tar.gz\n+ </package>\n+ <package sha256sum="cf61732ef9b38ecb6579055d1cd145198ad23a5a9ae4378f94a1494e6c56c884">\n+ https://depot.galaxyproject.org/software/data.table/data.table_1.10.0.tar.gz\n+ </package>\n+ <package sha256sum="d47be4430a1c343c20f9d3f67b8511506904e46be13ea4199769f012f1449209">\n+ https://depot.galaxyproject.org/software/GO.db/GO.db_3.4.0.tar.gz\n+ </package>\n+ <package sha256sum="dfccd4b4d6ec90cd7628fd128d2456d792f406cee4d32b13448dcb0ffe4ab056">\n+ https://depot.galaxyproject.org/software/NMF/NMF_0.20.6.tar.gz\n+ </package>\n+ <package sha256sum="7fa594d9576592e393283ec4fc79fd72128f663bd516e05651957ce1e6fe3c38">\n+ https://depot.galaxyproject.org/software/colorspace/colorspace_1.3-1.tar.gz\n+ </package>\n+ <package sha256sum="31151eaf36f70bdc1172da5ff5088ee51cc0a3db4ead59c7c38c25316d580dd1">\n+ https://depot.galaxyproject.org/software/dichromat/dichromat_2.0-0.tar.gz\n+ </package>\n+ <package sha256sum="7a4957c66ff622d7d1456adfbb728c60d406cdb2a754979797f9dcb0dc8fee99">\n+ https://depot.galaxyproject.org/software/fastmatch/fastmatch_1.0-4.tar.gz\n+ </package>\n+ <package sha256sum="5183e8dd7943df11c0f44460566adf06c03d5320f142699298f516d423b06ce1">\n+ https://depot.galaxyproject.org/software/irlba/irlba_2.1.2.tar.gz\n+ </package>\n+ <package sha256sum="19ad78c16bd5757333e7abbd5eebcec081deb494c9a4b6eec6919a3747b3386f">\n+ https://depot.galaxyproject.org/software/pkgmaker/pkgmaker_0.22.tar.gz\n+ </package>\n+ <package sha256sum="58a5c43b8012ca5e509fa29a8daf6f24f097b8eb021a723f6a9c33db1dd3f430">\n+ https://depot.galaxyproject.org/software/registry/registry_0.3.tar.gz\n+ </package>\n+ <package sha256sum="27019835b750f470b13dbb7fecd3b839a61b52774e23fffa191f919533768fb9">\n+ https://depot.galaxyproject.org/software/rngtools/rngtools_1.2.4.tar.gz\n+ </package>\n+ <package sha256sum="605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f">\n+ https://depot.galaxyproject.org/software/FDb.InfiniumMethylation.hg19/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz\n+ </package>\n+ </action>\n+ </actions>\n+ </install>\n+ </tool_dependency>\n' |