Mercurial > repos > testtool > get_geo

comparison getGEO/getGEO.R @ 11:2418fe6a0d12 draft

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author testtool
date Wed, 18 Jan 2017 11:35:14 -0500
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children fafbd5bb1f05
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10:b4f24cef49be 11:2418fe6a0d12
1 require("BiocGenerics", quietly = TRUE)
2 require("data.table", quietly = TRUE)
3 require("GEOquery", quietly = TRUE)
4 require("rtracklayer", quietly = TRUE)
5
6 options(warn = -1)
7 args <- commandArgs(trailingOnly = TRUE)
8 GSMTable = args[1]
9 MetaTable = args[2]
10 IlmnTable = args[3]
11 gmTable = args[4]
12
13 TAB = fread(GSMTable)
14
15 if (is.null(TAB)) {
16 stop("Must specify input files")
17 } else {
18 GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE)
19 IlmnIDTable <- Table(GEODataTable)
20 MetaData <- data.frame(Meta(GEODataTable))
21
22
23 write.csv(MetaData, MetaTable, row.names = FALSE, sep = "\t")
24 }
25
26 hm450.hg19 <- getPlatform()
27
28 IlmnInfo <-
29 data.table(
30 IlmnID = names(hm450.hg19),
31 CHR = as.data.frame(hm450.hg19@seqnames)$value,
32 BP = as.numeric(hm450.hg19@elementMetadata$probeStart)
33 )
34
35
36 write.csv(IlmnInfo, IlmnTable, row.names = FALSE, sep = "\t")
37
38
39 if (length(TAB$ID) > 1) {
40 mysamples <-
41 do.call("data.table", lapply(TAB$ID[-1], function(x)
42 Table(getGEO(x, getGPL = FALSE))[, -1]))
43
44 gmSet <- data.table(IlmnIDTable[, -1], mysamples)
45
46 } else {
47 gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE))
48 }
49
50
51 write.csv(gmSet, gmTable, row.names = FALSE, sep = "\t")