Mercurial > repos > davidvanzessen > combined_immune_repertoire_pipeline

comparison RScript.r @ 4:87fb14480352 draft

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Uploaded
author davidvanzessen
date Fri, 22 Nov 2013 08:12:53 -0500
parents 4e3df2384422
children 00d432c66fb8
comparison
equal deleted inserted replaced
3:2b1d3d6843e8 4:87fb14480352
3 args <- commandArgs(trailingOnly = TRUE) 3 args <- commandArgs(trailingOnly = TRUE)
4 4
5 inFile = args[1] 5 inFile = args[1]
6 outFile = args[2] 6 outFile = args[2]
7 outDir = args[3] 7 outDir = args[3]
8 clonalType = args[4]
8 9
9 if (!("gridExtra" %in% rownames(installed.packages()))) { 10 if (!("gridExtra" %in% rownames(installed.packages()))) {
10 install.packages("gridExtra", repos="http://cran.xl-mirror.nl/") 11 install.packages("gridExtra", repos="http://cran.xl-mirror.nl/")
11 } 12 }
12 library(gridExtra) 13 library(gridExtra)
31 32
32 test$Top.V.Gene = gsub("[*]([0-9]+)", "", test$Top.V.Gene) 33 test$Top.V.Gene = gsub("[*]([0-9]+)", "", test$Top.V.Gene)
33 test$Top.D.Gene = gsub("[*]([0-9]+)", "", test$Top.D.Gene) 34 test$Top.D.Gene = gsub("[*]([0-9]+)", "", test$Top.D.Gene)
34 test$Top.J.Gene = gsub("[*]([0-9]+)", "", test$Top.J.Gene) 35 test$Top.J.Gene = gsub("[*]([0-9]+)", "", test$Top.J.Gene)
35 36
36 test$VDJCDR3 = do.call(paste, c(test[c("Top.V.Gene", "Top.D.Gene", "Top.J.Gene","CDR3.Seq.DNA")], sep = ":")) 37 #test$VDJCDR3 = do.call(paste, c(test[c("Top.V.Gene", "Top.D.Gene", "Top.J.Gene","CDR3.Seq.DNA")], sep = ":"))
38 test$VDJCDR3 = do.call(paste, c(test[unlist(strsplit(clonalType, ","))], sep = ":"))
37 39
38 PROD = test[test$VDJ.Frame != "In-frame with stop codon" & test$VDJ.Frame != "Out-of-frame" & test$CDR3.Found.How != "NOT_FOUND" , ] 40 PROD = test[test$VDJ.Frame != "In-frame with stop codon" & test$VDJ.Frame != "Out-of-frame" & test$CDR3.Found.How != "NOT_FOUND" , ]
39 41
40 NONPROD = test[test$VDJ.Frame == "In-frame with stop codon" | test$VDJ.Frame == "Out-of-frame" | test$CDR3.Found.How == "NOT_FOUND" , ] 42 NONPROD = test[test$VDJ.Frame == "In-frame with stop codon" | test$VDJ.Frame == "Out-of-frame" | test$CDR3.Found.How == "NOT_FOUND" , ]
41 43