Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

diff RScript.r @ 14:1735e91a8f4b draft

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Uploaded
author davidvanzessen
date Thu, 05 Feb 2015 06:20:36 -0500
parents 576de7c96c4f
children d137974763b3
line wrap: on
line diff
--- a/RScript.r	Thu Jan 22 07:12:13 2015 -0500
+++ b/RScript.r	Thu Feb 05 06:20:36 2015 -0500
@@ -125,8 +125,8 @@
     both = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge[,paste(on, ".x", sep="")] > threshhold & patientMerge[,paste(on, ".y", sep="")] > threshhold)
     one = (grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene) & patient1[,on] > threshhold & !(patient1$CDR3_Sense_Sequence %in% patientMerge[both,]$CDR3_Sense_Sequence.x))
     two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$CDR3_Sense_Sequence %in% patientMerge[both,]$CDR3_Sense_Sequence.x))
-    read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count) + sum(patientMerge[both,]$normalized_read_count.x))
-    read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count) + sum(patientMerge[both,]$normalized_read_count.y))
+    read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count))
+    read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count))
     res1 = append(res1, sum(one))
     res2 = append(res2, sum(two))
     resBoth = append(resBoth, sum(both))
@@ -269,9 +269,9 @@
     two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$CDR3_Sense_Sequence %in% patientMerge[all,]$CDR3_Sense_Sequence.x))
     three = (grepl(V_Segment, patient3$V_Segment_Major_Gene) & grepl(J_Segment, patient3$J_Segment_Major_Gene) & patient3[,on] > threshhold & !(patient3$CDR3_Sense_Sequence %in% patientMerge[all,]$CDR3_Sense_Sequence.x))
     
-    read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.x))
-    read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.y))
-    read3Count = append(read3Count, sum(patient3[three,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.z))
+    read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count))
+    read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count))
+    read3Count = append(read3Count, sum(patient3[three,]$normalized_read_count))
     res1 = append(res1, sum(one))
     res2 = append(res2, sum(two))
     res3 = append(res3, sum(three))