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8
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1 args <- commandArgs(trailingOnly = TRUE)
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26
|
2
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|
8
|
3 GSE = args[1]
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|
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4 GSMTable = args[2]
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5
|
|
26
|
6
|
|
|
7
|
|
8
|
8 search1 <- entrez_search(db = "gds", term = GSE, retmax = 1)
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|
|
9
|
|
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10 rec2 <- entrez_summary(db = "gds",
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|
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11 id = search1$ids,
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12 version = "2.0")
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|
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13
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|
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14 extract <- extract_from_esummary(rec2,rownames(summary(rec2)))
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|
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15
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|
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16 samples <- extract$samples
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|
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17 colnames(samples)[which(names(samples) == "accession")] <- "ID"
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18 colnames(samples)[which(names(samples) == "title")] <- "Phenotype"
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|
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19
|
|
26
|
20 samples$Phenotype<-gsub("\\s", "",samples$Phenotype)
|
|
8
|
21
|
|
26
|
22 write.table(samples, GSMTable, row.names = FALSE,quote=FALSE,sep="\t")
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|
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23
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|
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24
|
