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8
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1 GSMTable <- ("test-data/GSMTable.txt")
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2 write.table(samples, GSMTable, row.names = FALSE, sep = "\t")
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3 ?write.table
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4 GSE <- "GSE51547"
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5 search1 <- entrez_search(db = "gds", term = GSE, retmax = 1)
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6 require("rentrez", quietly = TRUE)
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7 search1 <- entrez_search(db = "gds", term = GSE, retmax = 1)
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8 rec2 <- entrez_summary(db = "gds",
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9 id = search1$ids,
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10 version = "2.0")
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11 extract <- extract_from_esummary(rec2,rownames(summary(rec2)))
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12 samples <- extract$samples
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13 colnames(samples)[which(names(samples) == "accession")] <- "ID"
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14 colnames(samples)[which(names(samples) == "title")] <- "Phenotype"
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15 write.table(samples, GSMTable, row.names = FALSE, sep = "\t",quote = FALSE)
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16 write.table(samples, file=GSMTable.txt, row.names = FALSE, sep = "\t",quote = FALSE)
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17 write.table(samples, file="GSMTable.txt", row.names = FALSE, sep = "\t",quote = FALSE)
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28
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18 ??entrez_summary
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19 ??getGEO
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20 ??bumphunter
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21 ??annotatePeak
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