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comparison GRsetFromGEO/GRsetFromGEO.R @ 42:4987433afb56 draft

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author testtool
date Mon, 24 Apr 2017 10:09:39 -0400
parents 234e990e8e1d
children 660897ee0d12
comparison
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41:1ed398538e91 42:4987433afb56
1 require("BiocGenerics", quietly = TRUE)
2 require("data.table", quietly = TRUE)
3 require("GEOquery", quietly = TRUE)
1 require("minfi", quietly = TRUE) 4 require("minfi", quietly = TRUE)
2 require("GEOquery", quietly = TRUE)
3 require("FDb.InfiniumMethylation.hg19", quietly = TRUE) 5 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
4 6
5 args <- commandArgs(trailingOnly = TRUE) 7 args <- commandArgs(trailingOnly = TRUE)
6 GSE = args[1] 8 GSE = args[1]
7 output = args[2] 9 output = args[2]
22 annotation = default.450k.annotation 24 annotation = default.450k.annotation
23 what = c("Beta", "M") 25 what = c("Beta", "M")
24 mergeManifest = FALSE 26 mergeManifest = FALSE
25 i = 1 27 i = 1
26 28
27 gset <- getGEO(GSE) 29 gset <- GEOquery::getGEO(GSE)
28 gset <- gset[[1]] 30 gset <- gset[[1]]
29 31
30 platform <- annotation(gset) 32 platform <- annotation(gset)
31 33
32 ann <- getAnnotationString(c(array = array, annotation = annotation)) 34 ann <- getAnnotationString(c(array = array, annotation = annotation))