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comparison GRsetFromGEO/GRsetFromGEO.R @ 54:5752f23e451f draft

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author testtool
date Thu, 10 Aug 2017 06:20:22 -0400
parents fe7d4d8591c5
children e23909ae6676
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53:5547aeb4ff23 54:5752f23e451f
1 require(minfi, quietly = TRUE) 1 require(minfi, quietly = TRUE)
2 require(IlluminaHumanMethylation450kanno.ilmn12.hg19, quietly = TRUE)
3 2
4 options(warn = -1) 3 options(warn = -1)
5 options('download.file.method.GEOquery' = 'wget') 4 options('download.file.method.GEOquery' = 'wget')
6 options('GEOquery.inmemory.gpl'=FALSE) 5 options('GEOquery.inmemory.gpl'=FALSE)
7 6
8 7
9 args <- commandArgs(trailingOnly = TRUE) 8 args <- commandArgs(trailingOnly = TRUE)
10 input = args[1] 9 input = args[1]
11 output = args[2] 10 output = args[2]
12 11
13 GRset <- minfi::getGenomicRatioSetFromGEO(input) 12 GRset <- getGenomicRatioSetFromGEO(input)
14 13
15 save(GRset,file = output) 14 save(GRset,file = output)
16 15
17 ??getGenomicRatioSetFromGEO 16