Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/RScript.r @ 13:b45a74248628 draft

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author davidvanzessen
date Fri, 07 Aug 2015 05:52:21 -0400
parents 010402c959aa
children cf1def1aaa74
comparison
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12:010402c959aa 13:b45a74248628
111 un = paste(un, sep="\n") 111 un = paste(un, sep="\n")
112 writeLines(un, sampleFile) 112 writeLines(un, sampleFile)
113 close(sampleFile) 113 close(sampleFile)
114 114
115 # ---------------------- Counting the productive/unproductive and unique sequences ---------------------- 115 # ---------------------- Counting the productive/unproductive and unique sequences ----------------------
116
117 if(!("Functionality" %in% inputdata)){ #add a functionality column to the igblast data
118 inputdata$Functionality = "unproductive"
119 search = (inputdata$VDJ.Frame != "In-frame with stop codon" & inputdata$VDJ.Frame != "Out-of-frame" & inputdata$CDR3.Found.How != "NOT_FOUND")
120 if(sum(search) > 0){
121 inputdata[search,]$Functionality = "productive"
122 }
123 }
116 124
117 inputdata.dt = data.table(inputdata) #for speed 125 inputdata.dt = data.table(inputdata) #for speed
118 126
119 if(clonaltype == "none"){ 127 if(clonaltype == "none"){
120 ct = c("clonaltype") 128 ct = c("clonaltype")