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comparison GEO/getGEO.R @ 9:19ea355e26b3 draft

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author testtool
date Tue, 28 Feb 2017 05:11:54 -0500
parents 0647e033c218
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8:0647e033c218 9:19ea355e26b3
21 GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE) 21 GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE)
22 IlmnIDTable <- Table(GEODataTable) 22 IlmnIDTable <- Table(GEODataTable)
23 MetaData <- data.frame(Meta(GEODataTable)) 23 MetaData <- data.frame(Meta(GEODataTable))
24 24
25 25
26 write.csv(MetaData, protocol, row.names = FALSE, sep = "\t") 26 write.table(MetaData, protocol, row.names = FALSE, sep = "\t")
27 } 27 }
28 28
29 hm450.hg19 <- getPlatform() 29 hm450.hg19 <- getPlatform()
30 30
31 IlmnInfo <- 31 IlmnInfo <-
34 CHR = as.data.frame(hm450.hg19@seqnames)$value, 34 CHR = as.data.frame(hm450.hg19@seqnames)$value,
35 BP = as.numeric(hm450.hg19@elementMetadata$probeStart) 35 BP = as.numeric(hm450.hg19@elementMetadata$probeStart)
36 ) 36 )
37 37
38 38
39 write.csv(IlmnInfo, platform, row.names = FALSE, sep = "\t") 39 write.table(IlmnInfo, platform, row.names = FALSE, sep = "\t")
40 40
41 41
42 if (length(TAB$ID) > 1) { 42 if (length(TAB$ID) > 1) {
43 mysamples <- 43 mysamples <-
44 do.call("data.table", lapply(TAB$ID[-1], function(x) 44 do.call("data.table", lapply(TAB$ID[-1], function(x)