annotate getGSMdata/getGSMdata.R @ 33:ca4d7b65a2da draft

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author testtool
date Mon, 31 Jul 2017 11:56:42 -0400
parents 0051ff360c64
children faa0cd8ed36a
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1 require("rentrez", quietly = TRUE)
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3 args <- commandArgs(trailingOnly = TRUE)
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5 GSE = args[1]
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6 GSMTable = args[2]
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10 search1 <- entrez_search(db = "gds", term = GSE, retmax = 1)
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12 rec2 <- entrez_summary(db = "gds",
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13 id = search1$ids,
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14 version = "2.0")
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16 extract <- extract_from_esummary(rec2,rownames(summary(rec2)))
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18 samples <- extract$samples
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19 colnames(samples)[which(names(samples) == "accession")] <- "ID"
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20 colnames(samples)[which(names(samples) == "title")] <- "Phenotype"
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22 samples$Phenotype<-gsub("\\s", "",samples$Phenotype)
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24 write.table(samples, GSMTable, row.names = FALSE,quote=FALSE,sep="\t")
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