Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

changeset 64:39fff0180d41 draft

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Uploaded
author davidvanzessen
date Thu, 05 Nov 2015 09:07:03 -0500
parents 39ea37070e90
children 7a63e90cfc3d
files RScript.r
diffstat 1 files changed, 13 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/RScript.r	Wed Nov 04 11:02:01 2015 -0500
+++ b/RScript.r	Thu Nov 05 09:07:03 2015 -0500
@@ -618,6 +618,7 @@
                          Frequency = sum(rows.1$Frequency),
                          locus_V = rows.1[1,"locus_V"],
                          locus_J = rows.1[1,"locus_J"],
+                         uniqueID = rows.1[1,"uniqueID"],
                          normalized_read_count = sum(rows.1$normalized_read_count))
       sum.2 = sum.1[NULL,]
       rows.2 = patient.fuzzy[match.filter.2,]
@@ -639,6 +640,7 @@
                            Frequency = sum(rows.2$Frequency),
                            locus_V = rows.2[1,"locus_V"],
                            locus_J = rows.2[1,"locus_J"],
+                           uniqueID = rows.2[1,"uniqueID"],
                            normalized_read_count = sum(rows.2$normalized_read_count))
       }
 
@@ -662,6 +664,7 @@
                            Frequency = sum(rows.3$Frequency),
                            locus_V = rows.3[1,"locus_V"],
                            locus_J = rows.3[1,"locus_J"],
+                           uniqueID = rows.3[1,"uniqueID"],
                            normalized_read_count = sum(rows.3$normalized_read_count))
       }
 
@@ -716,7 +719,16 @@
 
       } else if(nrow(rows.1) > 1){
         patient1 = patient1[!(patient1$Clone_Sequence %in% rows.1$Clone_Sequence),]
-        patient1 = rbind(patient1, sum.1)
+        print(names(patient1)[names(patient1) %in% sum.1])
+        print(names(patient1)[!(names(patient1) %in% sum.1)])
+        print(names(patient1))
+        print(names(sum.1))
+        print(summary(sum.1))
+        print(summary(patient1))
+        print(dim(sum.1))
+        print(dim(patient1))
+        print(head(sum.1[,names(patient1)]))
+        patient1 = rbind(patient1, sum.1[,names(patient1)])
         patient.fuzzy = patient.fuzzy[-match.filter.1,]
       } else {
         patient.fuzzy = patient.fuzzy[-1,]