Mercurial > repos > testtool > get_geo
comparison getMETAdata/getMETAdata.R @ 38:608ab56a90d0 draft
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| author | testtool |
|---|---|
| date | Mon, 14 Aug 2017 09:21:07 -0400 |
| parents | |
| children |
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| 37:ec7a1f7f9a94 | 38:608ab56a90d0 |
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| 1 require("data.table", quietly = TRUE) | |
| 2 require("GEOquery", quietly = TRUE) | |
| 3 | |
| 4 | |
| 5 options(warn = -1) | |
| 6 options("download.file.method"="wget") | |
| 7 args <- commandArgs(trailingOnly = TRUE) | |
| 8 GSMTable = args[1] | |
| 9 MetaTable = args[2] | |
| 10 | |
| 11 TAB = fread(GSMTable) | |
| 12 | |
| 13 | |
| 14 if (is.null(TAB)) { | |
| 15 stop("Must specify input files") | |
| 16 } else { | |
| 17 options(download.file.method.GEOquery = "wget") | |
| 18 | |
| 19 | |
| 20 GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE) | |
| 21 MetaData <- data.frame(Meta(GEODataTable)) | |
| 22 | |
| 23 write.table(MetaData, MetaTable, row.names = FALSE, sep = "\t") | |
| 24 } | |
| 25 |