| Previous changeset 54:7aab6e28c62e (2017-04-25) Next changeset 56:d4c5ec2d87d5 (2017-04-28) |
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Commit message:
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added:
GRsetFromGEO/.Rapp.history GRsetFromGEO/.Rhistory GRsetFromGEO/._.DS_Store GRsetFromGEO/GRsetFromGEO.R GRsetFromGEO/GRsetFromGEO.xml GRsetFromGEO/test-data/._.DS_Store GRsetFromGEO/test-data/out.RData GRsetFromGEO/tool_dependencies.xml |
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removed:
getGEO/.Rhistory getGEO/._.DS_Store getGEO/getGEO.R getGEO/getGEO.xml getGEO/test-data/.Rhistory 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/test-data/out.RData getGEO/tool_dependencies.xml |
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| diff -r 7aab6e28c62e -r f84cadc1fdd6 GRsetFromGEO/.Rhistory --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GRsetFromGEO/.Rhistory Tue Apr 25 11:03:34 2017 -0400 |
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| @@ -0,0 +1,7 @@ +require("minfi", quietly = TRUE) +?require +require("minfi", quietly = TRUE) +minfi +as.data.frame(GRset) +GRset <- getGenomicRatioSetFromGEO(GSE) +getGenomicRatioSetFromGEO |
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| diff -r 7aab6e28c62e -r f84cadc1fdd6 GRsetFromGEO/._.DS_Store |
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| Binary file GRsetFromGEO/._.DS_Store has changed |
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| diff -r 7aab6e28c62e -r f84cadc1fdd6 GRsetFromGEO/GRsetFromGEO.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GRsetFromGEO/GRsetFromGEO.R Tue Apr 25 11:03:34 2017 -0400 |
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| @@ -0,0 +1,12 @@ +require("minfi", quietly = TRUE) + +options(warn = -1) +options("download.file.method"="wget") + +args <- commandArgs(trailingOnly = TRUE) +GSE = args[1] +output = args[2] + +GRset <- getGenomicRatioSetFromGEO(GSE) + +save(GRset,file = output) |
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| diff -r 7aab6e28c62e -r f84cadc1fdd6 GRsetFromGEO/GRsetFromGEO.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GRsetFromGEO/GRsetFromGEO.xml Tue Apr 25 11:03:34 2017 -0400 |
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| @@ -0,0 +1,36 @@ +<tool id="GetGEO" name="GRsetFromGEO" version="1.16.2"> + <description> + Reading Illumina methylation array data from GEO + </description> + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + </requirements> +<stdio> + <exit_code range="1:" /> +</stdio> + <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command> + <inputs> + <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> + </inputs> + <outputs> + <data format="RDdata" name="output" label="GRsetFromGEO.RData"/> + </outputs> + <tests> + <test> + <param name="test"> + <element name="test-data"> + <collection type="data"> + <element name="GSE" value="GSE51547"/> + </collection> + </element> + </param> + <output type="data" format="RData" name="output" label="test-data/out.RData"/> + </test> + </tests> + <help> +**Description** +</help> +<citations> +GEO +</citations> +</tool> |
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| diff -r 7aab6e28c62e -r f84cadc1fdd6 GRsetFromGEO/test-data/._.DS_Store |
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| Binary file GRsetFromGEO/test-data/._.DS_Store has changed |
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| diff -r 7aab6e28c62e -r f84cadc1fdd6 GRsetFromGEO/test-data/out.RData |
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| Binary file GRsetFromGEO/test-data/out.RData has changed |
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| diff -r 7aab6e28c62e -r f84cadc1fdd6 GRsetFromGEO/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GRsetFromGEO/tool_dependencies.xml Tue Apr 25 11:03:34 2017 -0400 |
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| b'@@ -0,0 +1,281 @@\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="e21c82b478dee4ed8a3e24f7afe9a8f1820c98e53c135f846a589a361cfaad3b">\n+ https://bioarchive.galaxyproject.org/BiocGenerics_0.21.1.tar.gz\n+ </package>\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/softwa'..b'project.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="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="605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f">\n+ https://depot.galaxyproject.org/software/FDb.InfiniumMethylation.hg19/FDb.InfiniumMethylation.hg19_2.2.0.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="cd26dbd60b2e2060541c4bb579ec1e0f6c262501431460b096b5fef323204432">\n+ https://bioarchive.galaxyproject.org/GEOquery_2.41.0.tar.gz\n+ </package>\n+ <package sha256sum="531aa7042bad9fc72d4b6868cc9f78fe24f5c27e36703c6be78d5eaf1b828ca1">\n+ https://bioarchive.galaxyproject.org/minfi_1.21.2.tar.gz\n+ </package>\n+ </action>\n+ </actions>\n+ </install>\n+ <readme>\n+ </readme>\n+</tool_dependency>\n' |
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| diff -r 7aab6e28c62e -r f84cadc1fdd6 getGEO/.Rhistory --- a/getGEO/.Rhistory Tue Apr 25 10:28:34 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r 7aab6e28c62e -r f84cadc1fdd6 getGEO/._.DS_Store |
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| Binary file getGEO/._.DS_Store has changed |
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| diff -r 7aab6e28c62e -r f84cadc1fdd6 getGEO/getGEO.R --- a/getGEO/getGEO.R Tue Apr 25 10:28:34 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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") - |
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| diff -r 7aab6e28c62e -r f84cadc1fdd6 getGEO/getGEO.xml --- a/getGEO/getGEO.xml Tue Apr 25 10:28:34 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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" "$Data_Table"</command> - <inputs> - <param optional="false" format="txt" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable"> - <validator type="empty_field" message="This field is required."/> - </param> - </inputs> - <outputs> - <data format="txt" name="protocol" label="protocol.txt"/> - <data format="txt" name="platform" label="platform.txt"/> - <data format="txt" name="Data_Table" label="Data_Table.txt"/> - </outputs> - <tests> - <test> - <param name="test"> - <element name="test-data"> - <collection type="data"> - <element name="GSMTable" value="test-data/input.txt" /> - </collection> - </element> - </param> - <output format="txt" name="protocol" label="test-data/protocol.txt"/> - <output format="txt" name="platform" label="test-data/platform.txt"/> - <output format="txt" name="Data_Table" label="test-data/Data_Table.txt"/> - </test> - </tests> - <help> -**Description** -</help> -<citations> -GEO -</citations> -</tool> |
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| diff -r 7aab6e28c62e -r f84cadc1fdd6 getGEO/test-data/.Rhistory --- a/getGEO/test-data/.Rhistory Tue Apr 25 10:28:34 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,512 +0,0 @@\n-what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <\n-0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1)\n-??getLocations\n-sampleNames(gset) <- gset$title\n-if (platform != "GPL13534")\n-warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",\n-platform))\n-if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <\n-0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))\n-warning("Values outside [0,1] detected. \'what\' argument should not be Beta.")\n-ann <- .getAnnotationString(c(array = array, annotation = annotation))\n-if (!require(ann, character.only = TRUE))\n-stop(sprintf("cannot load annotation package %s", ann))\n-getGenomicRatioSetFromGEO\n-object <- get(platform)\n-platform\n-gr <- getLocations(gset, mergeManifest = mergeManifest,\n-orderByLocation = TRUE)\n-gr <- getLocations(gset)\n-gset\n-gr <- getLocations(platform)\n-??getLocations\n-locusNames <- names(gset)\n-sampleNames(gset) <- gset$title\n-common <- intersect(locusNames, fData(gset)$Name)\n-if (length(common) == 0)\n-stop("No rowname matches. \'rownames\' need to match IlluminaHumanMethylation450k probe names.")\n-ind1 <- match(common, fData(gset)$Name)\n-ind2 <- match(common, locusNames)\n-preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))\n-if (what == "Beta") {\n-out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,\n-, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),\n-annotation = c(array = array, annotation = annotation),\n-preprocessMethod = preprocessing)\n-}\n-what\n-out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,\n-, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),\n-annotation = c(array = array, annotation = annotation),\n-preprocessMethod = preprocessing)\n-out <- GenomicRatioSet(gr = gset[ind2, ], Beta = exprs(gset)[ind1,\n-, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),\n-annotation = c(array = array, annotation = annotation),\n-preprocessMethod = preprocessing)\n-ind2\n-ind1\n-common\n-sampleNames(gset)\n-class(gmSet)\n-out <- GenomicRatioSet(gr = gmset, Beta = exprs(gset)[ind1,\n-, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),\n-annotation = c(array = array, annotation = annotation),\n-preprocessMethod = preprocessing)\n-if (length(TAB$ID) > 1) {\n-mysamples <-\n-do.call("data.table", lapply(TAB$ID[-1], function(x)\n-Table(getGEO(x, getGPL = FALSE))[, -1]))\n-gmSet <- data.table(IlmnIDTable[, -1], mysamples)\n-} else {\n-gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE))\n-}\n-out <- GenomicRatioSet(gr = gmset, Beta = exprs(gset)[ind1,\n-, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),\n-annotation = c(array = array, annotation = annotation),\n-preprocessMethod = preprocessing)\n-out <- GenomicRatioSet(gr = gmSet, Beta = exprs(gset)[ind1,\n-, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),\n-annotation = c(array = array, annotation = annotation),\n-preprocessMethod = preprocessing)\n-??GenomicRatioSet\n-sampleNames(gset)\n-common\n-class(gset)\n-??GenomicRatioSet\n-GenomicRatioSet\n-getGenomicRatioSetFromGEO\n-GSE <- "GSE51547"\n-function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",\n-annotation = .default.450k.annotation, what = c("Beta", "M"),\n-mergeManifest = FALSE, i = 1)\n-{\n-what <- match.arg(what)\n-if (is.null(GSE) && is.null(path))\n-stop("Either GSE or path must be supplied.")\n-if (!is.null(GSE))\n-gset <- GEOquery::getGEO(GSE)\n-else gset <- GEOquery::getGEO(filename = file.path(path,\n-list.files(path, pattern = ".soft")))\n-if (length(gset) == 0)\n-stop("Empty list retrieved from GEO.")\n-if (length(gset) > 1) {\n-warning("More than one ExpressionSet found:\\n", names(gset),\n-"\\nUsing entry ", i)\n-gset <- gset[[i]]\n-}\n-else gset <- gset[[1]]\n-platform <- annotation(gset)\n-if (platform != "GPL13534")\n-warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",\n-platform))\n-if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <\n-0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))\n-warnin'..b'ated with IlluminaHumanMethylation450k. Should be GPL13534.",\n-platform))\n-if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <\n-0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))\n-warning("Values outside [0,1] detected. \'what\' argument should not be Beta.")\n-ann <- .getAnnotationString(c(array = array, annotation = annotation))\n-if (!require(ann, character.only = TRUE))\n-stop(sprintf("cannot load annotation package %s", ann))\n-object <- get(ann)\n-gr <- getLocations(object, mergeManifest = mergeManifest,\n-orderByLocation = TRUE)\n-locusNames <- names(gr)\n-sampleNames(gset) <- gset$title\n-common <- intersect(locusNames, fData(gset)$Name)\n-if (length(common) == 0)\n-stop("No rowname matches. \'rownames\' need to match IlluminaHumanMethylation450k probe names.")\n-ind1 <- match(common, fData(gset)$Name)\n-ind2 <- match(common, locusNames)\n-preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))\n-if (what == "Beta") {\n-out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,\n-, drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),\n-annotation = c(array = array, annotation = annotation),\n-preprocessMethod = preprocessing)\n-}\n-else {\n-out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,\n-M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,\n-pData = pData(gset), annotation = c(array = array,\n-annotation = annotation), preprocessMethod = preprocessing)\n-}\n-save(out,output)\n-}\n-out\n-what\n-function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",\n-annotation = .default.450k.annotation, what = c("Beta", "M"),\n-mergeManifest = FALSE, i = 1)\n-what <- match.arg(what)\n-if (length(gset) == 0)\n-stop("Empty list retrieved from GEO.")\n-if (length(gset) > 1) {\n-warning("More than one ExpressionSet found:\\n", names(gset),\n-"\\nUsing entry ", i)\n-gset <- gset[[i]]\n-if (length(gset) == 0) {\n-stop("Empty list retrieved from GEO.")\n-} if (length(gset) > 1) {\n-warning("More than one ExpressionSet found:\\n", names(gset),\n-"\\nUsing entry ", i)}\n-if (length(gset) == 0)\n-stop("Empty list retrieved from GEO.")\n-if (length(gset) > 1) {\n-warning("More than one ExpressionSet found:\\n", names(gset),\n-"\\nUsing entry ", i)\n-gset <- gset[[i]]}\n-gset\n-else gset <- gset[[1]]\n-gset <- gset[[1]]\n-gset\n-gset <- gset[[i]]}\n-gset <- getGEO(GSE)\n-1gset <- gset[[i]]\n-if (length(gset) == 0)\n-stop("Empty list retrieved from GEO.")\n-if (length(gset) > 1) {\n-warning("More than one ExpressionSet found:\\n", names(gset),\n-"\\nUsing entry ", i)\n-1gset <- gset[[i]]\n-if (length(gset) == 0)\n-stop("Empty list retrieved from GEO.")\n-if (length(gset) > 1) {\n-warning("More than one ExpressionSet found:\\n", names(gset),\n-"\\nUsing entry ", i)\n-1gset <- gset[[i]]\n-if (length(gset) == 0)\n-stop("Empty list retrieved from GEO.")\n-if (length(gset) > 1) {\n-warning("More than one ExpressionSet found:\\n", names(gset),\n-"\\nUsing entry ", i)\n-gset <- gset[[i]]\n-if (length(gset) == 0)\n-stop("Empty list retrieved from GEO.")\n-if (length(gset) > 1) {\n-warning("More than one ExpressionSet found:\\n", names(gset),\n-"\\nUsing entry ", i)\n-gset <- gset[[i]]}\n-if (length(gset) == 0)\n-stop("Empty list retrieved from GEO.")\n-if (length(gset) > 1) {\n-warning("More than one ExpressionSet found:\\n", names(gset),\n-"\\nUsing entry ", i)\n-gset <- gset[[i]]}\n-if (length(gset) == 0) {\n-stop("Empty list retrieved from GEO.")\n-if (length(gset) > 1) {\n-warning("More than one ExpressionSet found:\\n", names(gset),\n-"\\nUsing entry ", i)\n-gset <- gset[[i]]}}\n-if (length(gset) == 0) {\n-stop("Empty list retrieved from GEO.")\n-if (length(gset) > 1) {\n-warning("More than one ExpressionSet found:\\n", names(gset),\n-"\\nUsing entry ", i)\n-gset <- gset[[i]]}}}\n-# else\n-gset\n-class(gset)\n-ann <- .getAnnotationString(c(array = array, annotation = annotation))\n-.getAnnotationString\n-getAnnotationString\n-??annotation\n-ann <- .getAnnotationString(c(array = array, annotation = annotation))\n-if (!require(ann, character.only = TRUE))\n-stop(sprintf("cannot load annotation package %s", ann))\n-object <- get(ann)\n' |
| b |
| diff -r 7aab6e28c62e -r f84cadc1fdd6 getGEO/test-data/._.DS_Store |
| b |
| Binary file getGEO/test-data/._.DS_Store has changed |
| b |
| diff -r 7aab6e28c62e -r f84cadc1fdd6 getGEO/test-data/._input.csv |
| b |
| Binary file getGEO/test-data/._input.csv has changed |
| b |
| diff -r 7aab6e28c62e -r f84cadc1fdd6 getGEO/test-data/IlmnTable.txt --- a/getGEO/test-data/IlmnTable.txt Tue Apr 25 10:28:34 2017 -0400 +++ /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 7aab6e28c62e -r f84cadc1fdd6 getGEO/test-data/MetaTable.txt --- a/getGEO/test-data/MetaTable.txt Tue Apr 25 10:28:34 2017 -0400 +++ /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 7aab6e28c62e -r f84cadc1fdd6 getGEO/test-data/gmTable.txt --- a/getGEO/test-data/gmTable.txt Tue Apr 25 10:28:34 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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|
| b |
| diff -r 7aab6e28c62e -r f84cadc1fdd6 getGEO/test-data/input.csv --- a/getGEO/test-data/input.csv Tue Apr 25 10:28:34 2017 -0400 +++ /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 7aab6e28c62e -r f84cadc1fdd6 getGEO/test-data/out.RData |
| b |
| Binary file getGEO/test-data/out.RData has changed |
| b |
| diff -r 7aab6e28c62e -r f84cadc1fdd6 getGEO/tool_dependencies.xml --- a/getGEO/tool_dependencies.xml Tue Apr 25 10:28:34 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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