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