| 1 | #Merge all gene counts from run 1
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| 2 | #Date 06-Nov-2013
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| 3 |
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| 4 | setwd("/virdir/Backup/run_1_gene_counts")
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| 5 | datadir <- "/virdir/Backup/run_1_gene_counts/run_1_gene_counts"
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| 6 | filelist <- dir(datadir)
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| 7 |
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| 8 | length(filelist) #2330
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| 9 |
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| 10 |
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| 11 | temp <- read.table(paste(datadir,filelist[1], sep="/"), as.is=T, header=T, row.names=1)
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| 12 |
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| 13 | for(i in 2:length(filelist))
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| 14 | {
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| 15 | temp2 <-read.table(paste(datadir,filelist[i], sep="/"), as.is=T, header=T, row.names=1)
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| 16 | temp <- cbind(temp, temp2[,1])
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| 17 | print(i)
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| 18 | }
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| 19 | dim(temp)
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| 20 | #add colnames
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| 21 | sample_names <- c()
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| 22 | for (i in 1:length(filelist))
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| 23 | {
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| 24 | sample_names[i] <- strsplit(filelist[i], "\\.")[[1]][1]
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| 25 | }
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| 26 |
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| 27 | colnames(temp) <- sample_names
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| 28 |
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| 29 | write.table(temp, file="combined_gene_count_run_1.txt", sep="\t", quote=F, row.names=T)
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| 30 |
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