Mercurial > repos > testtool > get_geo
view GEO/getGEO.R @ 34:6025fa3bfc40 draft
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author | testtool |
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date | Thu, 09 Feb 2017 09:54:46 -0500 |
parents | 2b223a449cf6 |
children | a266a7c268e9 |
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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(warn = -1,"download.file.method"="wget") args <- commandArgs(trailingOnly = TRUE) GSMTable = args[1] MetaTable = args[2] IlmnTable = args[3] gmTable = args[4] TAB = fread(GSMTable) if (is.null(TAB)) { stop("Must specify input files") } else { GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE) IlmnIDTable <- Table(GEODataTable) MetaData <- data.frame(Meta(GEODataTable)) write.csv(MetaData, MetaTable, row.names = FALSE, sep = "\t") } hm450.hg19 <- getPlatform() IlmnInfo <- data.table( IlmnID = names(hm450.hg19), CHR = as.data.frame(hm450.hg19@seqnames)$value, BP = as.numeric(hm450.hg19@elementMetadata$probeStart) ) write.csv(IlmnInfo, IlmnTable, row.names = FALSE, sep = "\t") if (length(TAB$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.csv(gmSet, gmTable, row.names = FALSE, sep = "\t")