Mercurial > repos > testtool > get_gr_set
comparison GRsetFromGEO/GRsetFromGEO.R @ 39:05f6acc80f47 draft
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| author | testtool |
|---|---|
| date | Mon, 07 Aug 2017 09:53:59 -0400 |
| parents | 88d2c717105e |
| children | fe7d4d8591c5 |
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| 38:88d2c717105e | 39:05f6acc80f47 |
|---|---|
| 1 require(minfi, quietly = TRUE) | |
| 2 require(IlluminaHumanMethylation450kanno.ilmn12.hg19, quietly = TRUE) | |
| 3 | |
| 1 options(warn = -1) | 4 options(warn = -1) |
| 2 options('download.file.method.GEOquery' = 'wget') | 5 options('download.file.method.GEOquery' = 'wget') |
| 3 options('GEOquery.inmemory.gpl'=FALSE) | 6 options('GEOquery.inmemory.gpl'=FALSE) |
| 4 | 7 |
| 5 | 8 |
| 6 args <- commandArgs(trailingOnly = TRUE) | 9 args <- commandArgs(trailingOnly = TRUE) |
| 7 input = args[1] | 10 input = args[1] |
| 8 output = args[2] | 11 output = args[2] |
| 9 input <- 'GSE51547' | 12 |
| 10 GRset <- getGenomicRatioSetFromGEO(input) | 13 GRset <- getGenomicRatioSetFromGEO(input) |
| 11 | 14 |
| 12 save(GRset,file = output) | 15 save(GRset,file = output) |
| 13 | 16 |