# HG changeset patch
# User davidvanzessen
# Date 1446194373 14400
# Node ID 77a090cd0e028dce8b4db0b5c43b63139d3c12bb
# Parent  28c3695259c14b34459f0e9586e4f5bf71c1597a
Uploaded

diff -r 28c3695259c1 -r 77a090cd0e02 RScript.r
--- a/RScript.r	Thu Oct 29 11:21:33 2015 -0400
+++ b/RScript.r	Fri Oct 30 04:39:33 2015 -0400
@@ -442,14 +442,14 @@
 interval = intervalFreq
 intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval))
 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
-lapply(patients[4], FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
+lapply(patients, FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
 
 cat("<tr><td>Starting Cell Count analysis</td></tr>", file=logfile, append=T)
 
 interval = intervalReads
 intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval))
 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
-lapply(patients[4], FUN=patientCountOnColumn, product = product, interval=interval, on="normalized_read_count")
+lapply(patients, FUN=patientCountOnColumn, product = product, interval=interval, on="normalized_read_count")
 
 if(nrow(single_patients) > 0){
 	scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
@@ -971,12 +971,12 @@
   one = triplets[triplets$Sample == "14696_reg_BM",]
   two = triplets[triplets$Sample == "24536_reg_BM",]
   three = triplets[triplets$Sample == "24062_reg_BM",]
-  #tripletAnalysis(one, "14696_1_Trio", two, "14696_2_Trio", three, "14696_3_Trio", product=product, interval=interval, on="normalized_read_count", T)
+  tripletAnalysis(one, "14696_1_Trio", two, "14696_2_Trio", three, "14696_3_Trio", product=product, interval=interval, on="normalized_read_count", T)
   
   one = triplets[triplets$Sample == "16278_Left",]
   two = triplets[triplets$Sample == "26402_Left",]
   three = triplets[triplets$Sample == "26759_Left",]
-  #tripletAnalysis(one, "16278_Left_Trio", two, "26402_Left_Trio", three, "26759_Left_Trio", product=product, interval=interval, on="normalized_read_count", T)
+  tripletAnalysis(one, "16278_Left_Trio", two, "26402_Left_Trio", three, "26759_Left_Trio", product=product, interval=interval, on="normalized_read_count", T)
   
   one = triplets[triplets$Sample == "16278_Right",]
   two = triplets[triplets$Sample == "26402_Right",]
@@ -992,12 +992,12 @@
   one = triplets[triplets$Sample == "14696_reg_BM",]
   two = triplets[triplets$Sample == "24536_reg_BM",]
   three = triplets[triplets$Sample == "24062_reg_BM",]
-  #tripletAnalysis(one, "14696_1_Trio", two, "14696_2_Trio", three, "14696_3_Trio", product=product, interval=interval, on="Frequency", F)
+  tripletAnalysis(one, "14696_1_Trio", two, "14696_2_Trio", three, "14696_3_Trio", product=product, interval=interval, on="Frequency", F)
   
   one = triplets[triplets$Sample == "16278_Left",]
   two = triplets[triplets$Sample == "26402_Left",]
   three = triplets[triplets$Sample == "26759_Left",]
-  #tripletAnalysis(one, "16278_Left_Trio", two, "26402_Left_Trio", three, "26759_Left_Trio", product=product, interval=interval, on="Frequency", F)
+  tripletAnalysis(one, "16278_Left_Trio", two, "26402_Left_Trio", three, "26759_Left_Trio", product=product, interval=interval, on="Frequency", F)
   
   one = triplets[triplets$Sample == "16278_Right",]
   two = triplets[triplets$Sample == "26402_Right",]