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comparison GEO/getGEO.R @ 32:2b223a449cf6 draft

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author testtool
date Thu, 09 Feb 2017 08:56:42 -0500
parents eb1a8cedf6c5
children a266a7c268e9
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31:f81cbc34657c 32:2b223a449cf6
2 require("data.table", quietly = TRUE) 2 require("data.table", quietly = TRUE)
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,"download.file.method"="wget")
8
8 args <- commandArgs(trailingOnly = TRUE) 9 args <- commandArgs(trailingOnly = TRUE)
9 GSMTable = args[1] 10 GSMTable = args[1]
10 MetaTable = args[2] 11 MetaTable = args[2]
11 IlmnTable = args[3] 12 IlmnTable = args[3]
12 gmTable = args[4] 13 gmTable = args[4]