Mercurial > repos > testtool > get_gr_set
comparison GRsetFromGEO/GRsetFromGEO.R @ 38:88d2c717105e draft
Uploaded
| author | testtool |
|---|---|
| date | Mon, 24 Jul 2017 10:39:43 -0400 |
| parents | ae82fab7c544 |
| children | 05f6acc80f47 |
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| 37:10996f6ddcb5 | 38:88d2c717105e |
|---|---|
| 1 require("IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE) | |
| 2 require("minfi", quietly = TRUE) | |
| 3 | |
| 4 options(warn = -1) | 1 options(warn = -1) |
| 5 options('download.file.method.GEOquery' = 'wget') | 2 options('download.file.method.GEOquery' = 'wget') |
| 6 options('GEOquery.inmemory.gpl'=FALSE) | 3 options('GEOquery.inmemory.gpl'=FALSE) |
| 7 | 4 |
| 8 | 5 |
| 9 args <- commandArgs(trailingOnly = TRUE) | 6 args <- commandArgs(trailingOnly = TRUE) |
| 10 input = args[1] | 7 input = args[1] |
| 11 output = args[2] | 8 output = args[2] |
| 12 | 9 input <- 'GSE51547' |
| 13 GRset <- getGenomicRatioSetFromGEO(input) | 10 GRset <- getGenomicRatioSetFromGEO(input) |
| 14 | 11 |
| 15 save(GRset,file = output) | 12 save(GRset,file = output) |
| 13 |