Mercurial > repos > testtool > get_geo

comparison getGEO/getGEO.R @ 26:b342a87d7c03 draft

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author testtool
date Mon, 06 Feb 2017 09:44:29 -0500
parents fe105dbd7e1e
children 315b0dc61049
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25:e44ea6de2d4f 26:b342a87d7c03
3 require("GEOquery", quietly = TRUE) 3 require("GEOquery", quietly = TRUE)
4 require("rtracklayer", quietly = TRUE) 4 require("rtracklayer", quietly = TRUE)
5 require("FDb.InfiniumMethylation.hg19", quietly = TRUE) 5 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
6 6
7 options(warn = -1) 7 options(warn = -1)
8 options("download.file.method"="wget")
9 args <- commandArgs(trailingOnly = TRUE) 8 args <- commandArgs(trailingOnly = TRUE)
10 GSMTable = args[1] 9 GSMTable = args[1]
11 MetaTable = args[2] 10 MetaTable = args[2]
12 IlmnTable = args[3] 11 IlmnTable = args[3]
13 gmTable = args[4] 12 gmTable = args[4]