Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/RScript.r @ 50:2a79f9adf89b draft

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Uploaded
author davidvanzessen
date Wed, 27 Jan 2016 10:48:31 -0500
parents d08dfc8d5225
children 371c568408e9
comparison
equal deleted inserted replaced
49:188712b1735f 50:2a79f9adf89b
41 locus = args[6] # IGH, IGK, IGL, TRB, TRA, TRG or TRD 41 locus = args[6] # IGH, IGK, IGL, TRB, TRA, TRG or TRD
42 filterproductive = ifelse(args[7] == "yes", T, F) #should unproductive sequences be filtered out? (yes/no) 42 filterproductive = ifelse(args[7] == "yes", T, F) #should unproductive sequences be filtered out? (yes/no)
43 clonality_method = args[8] 43 clonality_method = args[8]
44 filter_uniques = args[9] 44 filter_uniques = args[9]
45 45
46 print(paste("filter_uniques", filter_uniques))
47
46 # ---------------------- Data preperation ---------------------- 48 # ---------------------- Data preperation ----------------------
47 49
48 print("Report Clonality - Data preperation") 50 print("Report Clonality - Data preperation")
49 51
50 inputdata = read.table(infile, sep="\t", header=TRUE, fill=T, comment.char="") 52 inputdata = read.table(infile, sep="\t", header=TRUE, fill=T, comment.char="")
61 63
62 #filter uniques 64 #filter uniques
63 inputdata.removed = inputdata[NULL,] 65 inputdata.removed = inputdata[NULL,]
64 66
65 filter_uniques = filter_uniques == "yes" && c("CDR1.Seq", "CDR2.Seq", "CDR3.Seq", "FR1.IMGT", "FR2.IMGT", "FR3.IMGT") %in% names(inputdata) 67 filter_uniques = filter_uniques == "yes" && c("CDR1.Seq", "CDR2.Seq", "CDR3.Seq", "FR1.IMGT", "FR2.IMGT", "FR3.IMGT") %in% names(inputdata)
68
69 print(paste("filter_uniques", filter_uniques))
66 70
67 if(filter_uniques){ 71 if(filter_uniques){
68 72
69 clmns = names(inputdata) 73 clmns = names(inputdata)
70 74