|
6
|
1 require("BiocGenerics", quietly = TRUE)
|
|
|
2 require("data.table", quietly = TRUE)
|
|
|
3 require("GEOquery", quietly = TRUE)
|
|
|
4 require("rtracklayer", quietly = TRUE)
|
|
|
5 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
|
|
|
6
|
|
|
7 options("download.file.method.GEOquery"="wget")
|
|
|
8 options(warn = -1)
|
|
|
9
|
|
|
10 args <- commandArgs(trailingOnly = TRUE)
|
|
|
11 GSMTable = args[1]
|
|
|
12 MetaTable = args[2]
|
|
|
13 IlmnTable = args[3]
|
|
|
14 gmTable = args[4]
|
|
|
15
|
|
|
16 TAB = fread(GSMTable)
|
|
|
17
|
|
|
18 if (is.null(TAB)) {
|
|
|
19 stop("Must specify input files")
|
|
|
20 } else {
|
|
|
21 GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE)
|
|
|
22 IlmnIDTable <- Table(GEODataTable)
|
|
|
23 MetaData <- data.frame(Meta(GEODataTable))
|
|
|
24
|
|
|
25
|
|
|
26 write.csv(MetaData, MetaTable, row.names = FALSE, sep = "\t")
|
|
|
27 }
|
|
|
28
|
|
|
29 hm450.hg19 <- getPlatform()
|
|
|
30
|
|
|
31 IlmnInfo <-
|
|
|
32 data.table(
|
|
|
33 IlmnID = names(hm450.hg19),
|
|
|
34 CHR = as.data.frame(hm450.hg19@seqnames)$value,
|
|
|
35 BP = as.numeric(hm450.hg19@elementMetadata$probeStart)
|
|
|
36 )
|
|
|
37
|
|
|
38
|
|
|
39 write.csv(IlmnInfo, IlmnTable, row.names = FALSE, sep = "\t")
|
|
|
40
|
|
|
41
|
|
|
42 if (length(TAB$ID) > 1) {
|
|
|
43 mysamples <-
|
|
|
44 do.call("data.table", lapply(TAB$ID[-1], function(x)
|
|
|
45 Table(getGEO(x, getGPL = FALSE))[, -1]))
|
|
|
46
|
|
|
47 gmSet <- data.table(IlmnIDTable[, -1], mysamples)
|
|
|
48
|
|
|
49 } else {
|
|
|
50 gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE))
|
|
|
51 }
|
|
|
52
|
|
|
53
|
|
|
54 write.csv(gmSet, gmTable, row.names = FALSE, sep = "\t")
|
