Mercurial > repos > testtool > geo_data
view getGEO/getGEO.R @ 10:cbc8174bd361 draft
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author | testtool |
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date | Mon, 20 Mar 2017 06:54:27 -0400 |
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children | fc93085430a8 |
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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")