Mercurial > repos > davidvanzessen > mutation_analysis

comparison naive_output.r @ 69:7acdcd5c52ef draft

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Uploaded
author davidvanzessen
date Fri, 22 Apr 2016 05:07:10 -0400
parents 099cc1254f74
children c2e1d5a93f98
comparison
equal deleted inserted replaced
68:3636d5aaa127 69:7acdcd5c52ef
1 args <- commandArgs(trailingOnly = TRUE) 1 args <- commandArgs(trailingOnly = TRUE)
2 2
3 naive.file = args[1] 3 naive.file = args[1]
4 shm.file = args[2] 4 shm.file = args[2]
5 output.file = args[3] 5 output.file.ca = args[3]
6 output.file.cg = args[4]
7 output.file.cm = args[5]
6 8
7 naive = read.table(naive.file, sep="\t", header=T, quote="", fill=T) 9 naive = read.table(naive.file, sep="\t", header=T, quote="", fill=T)
8 shm.merge = read.table(shm.file, sep="\t", header=T, quote="", fill=T) 10 shm.merge = read.table(shm.file, sep="\t", header=T, quote="", fill=T)
9 11
10 12
12 print(paste("nrow final:", nrow(final))) 14 print(paste("nrow final:", nrow(final)))
13 names(final)[names(final) == "best_match"] = "Sample" 15 names(final)[names(final) == "best_match"] = "Sample"
14 final.numeric = final[,sapply(final, is.numeric)] 16 final.numeric = final[,sapply(final, is.numeric)]
15 final.numeric[is.na(final.numeric)] = 0 17 final.numeric[is.na(final.numeric)] = 0
16 final[,sapply(final, is.numeric)] = final.numeric 18 final[,sapply(final, is.numeric)] = final.numeric
17 print(paste("nrow final:", nrow(final)))
18 final2 = final
19 final2$Sample = gsub("[0-9]", "", final2$Sample)
20 final = rbind(final, final2)
21 final$Replicate = 1
22 19
23 write.table(final, output.file, quote=F, sep="\t", row.names=F, col.names=T) 20 final.ca = final[grepl("ca", final$Sample),]
21 final.cg = final[grepl("cg", final$Sample),]
22 final.cm = final[grepl("cm", final$Sample),]
23
24
25
26 #print(paste("nrow final:", nrow(final)))
27 #final2 = final
28 #final2$Sample = gsub("[0-9]", "", final2$Sample)
29 #final = rbind(final, final2)
30 #final$Replicate = 1
31
32 write.table(final.ca, output.file.ca, quote=F, sep="\t", row.names=F, col.names=T)
33 write.table(final.cg, output.file.cg, quote=F, sep="\t", row.names=F, col.names=T)
34 write.table(final.cm, output.file.cm, quote=F, sep="\t", row.names=F, col.names=T)