Mercurial > repos > davidvanzessen > mutation_analysis

changeset 7:cb7c65e3e43f draft

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Uploaded
author davidvanzessen
date Wed, 11 Mar 2015 08:56:37 -0400
parents 3c2230868300
children 3f4b4ef46c7f
files mutation_analysis.r
diffstat 1 files changed, 15 insertions(+), 39 deletions(-) [+]
line wrap: on
line diff
--- a/mutation_analysis.r	Wed Mar 11 06:01:45 2015 -0400
+++ b/mutation_analysis.r	Wed Mar 11 08:56:37 2015 -0400
@@ -102,23 +102,17 @@
   dat[is.na(dat[,col]),] = 0
 }
 
-dat$VRegionMutations =  dat$FR1.IMGT.Nb.of.mutations + 
-                        dat$CDR1.IMGT.Nb.of.mutations + 
+dat$VRegionMutations =  dat$CDR1.IMGT.Nb.of.mutations + 
                         dat$FR2.IMGT.Nb.of.mutations + 
                         dat$CDR2.IMGT.Nb.of.mutations +
                         dat$FR3.IMGT.Nb.of.mutations
 
-dat$VRegionNucleotides =  dat$FR1.IMGT.Nb.of.nucleotides +
-                          dat$CDR1.IMGT.Nb.of.nucleotides +
+dat$VRegionNucleotides =  dat$CDR1.IMGT.Nb.of.nucleotides +
                           dat$FR2.IMGT.Nb.of.nucleotides +
                           dat$CDR2.IMGT.Nb.of.nucleotides +
                           dat$FR3.IMGT.Nb.of.nucleotides
 
-dat$transitionMutations = dat$FR1.IMGT.a.g +
-                          dat$FR1.IMGT.g.a +
-                          dat$FR1.IMGT.c.t +
-                          dat$FR1.IMGT.t.c +
-                          dat$CDR1.IMGT.a.g +
+dat$transitionMutations = dat$CDR1.IMGT.a.g +
                           dat$CDR1.IMGT.g.a +
                           dat$CDR1.IMGT.c.t +
                           dat$CDR1.IMGT.t.c +
@@ -135,15 +129,7 @@
                           dat$FR3.IMGT.c.t +
                           dat$FR3.IMGT.t.c
 
-dat$transversionMutations = dat$FR1.IMGT.a.c +
-                            dat$FR1.IMGT.c.a +
-                            dat$FR1.IMGT.a.t +
-                            dat$FR1.IMGT.t.a +
-                            dat$FR1.IMGT.g.c +
-                            dat$FR1.IMGT.c.g +
-                            dat$FR1.IMGT.g.t +
-                            dat$FR1.IMGT.t.g +
-                            dat$CDR1.IMGT.a.c +
+dat$transversionMutations = dat$CDR1.IMGT.a.c +
                             dat$CDR1.IMGT.c.a +
                             dat$CDR1.IMGT.a.t +
                             dat$CDR1.IMGT.t.a +
@@ -177,9 +163,7 @@
                             dat$FR3.IMGT.t.g
 
 
-dat$transitionMutationsAtGC = dat$FR1.IMGT.g.a +
-                              dat$FR1.IMGT.c.t +
-                              dat$CDR1.IMGT.g.a +
+dat$transitionMutationsAtGC = dat$CDR1.IMGT.g.a +
                               dat$CDR1.IMGT.c.t +
                               dat$FR2.IMGT.g.a +
                               dat$FR2.IMGT.c.t +
@@ -188,13 +172,7 @@
                               dat$FR3.IMGT.g.a +
                               dat$FR3.IMGT.c.t
 
-dat$totalMutationsAtGC = dat$FR1.IMGT.g.a +
-                         dat$FR1.IMGT.c.t +
-                         dat$FR1.IMGT.c.a +
-                         dat$FR1.IMGT.g.c +
-                         dat$FR1.IMGT.c.g +
-                         dat$FR1.IMGT.g.t +
-                         dat$CDR1.IMGT.g.a +
+dat$totalMutationsAtGC = dat$CDR1.IMGT.g.a +
                          dat$CDR1.IMGT.c.t +
                          dat$CDR1.IMGT.c.a +
                          dat$CDR1.IMGT.g.c +
@@ -270,16 +248,15 @@
       }
       NT1 = LETTERS[letters == nt1]
       NT2 = LETTERS[letters == nt2]
-      FR1 = paste("FR1.IMGT.", nt1, ".", nt2, sep="")
+      FR1 = 0 #paste("FR1.IMGT.", nt1, ".", nt2, sep="")
       CDR1 = paste("CDR1.IMGT.", nt1, ".", nt2, sep="")
       FR2 = paste("FR2.IMGT.", nt1, ".", nt2, sep="")
       CDR2 = paste("CDR2.IMGT.", nt1, ".", nt2, sep="")
       FR3 = paste("FR3.IMGT.", nt1, ".", nt2, sep="")
-      transitionTable[NT1,NT2] = sum( tmp[,FR1] + 
-                                        tmp[,CDR1] +
-                                        tmp[,FR2] +
-                                        tmp[,CDR2] +
-                                        tmp[,FR3])
+      transitionTable[NT1,NT2] = sum( tmp[,CDR1] +
+                                      tmp[,FR2] +
+                                      tmp[,CDR2] +
+                                      tmp[,FR3])
     }
   }
   write.table(x=transitionTable, file=paste("transitions_", gene ,".txt", sep=""), sep=",",quote=F,row.names=T,col.names=NA)
@@ -332,11 +309,10 @@
 		FR2 = paste("FR2.IMGT.", nt1, ".", nt2, sep="")
 		CDR2 = paste("CDR2.IMGT.", nt1, ".", nt2, sep="")
 		FR3 = paste("FR3.IMGT.", nt1, ".", nt2, sep="")
-		transitionTable[NT1,NT2] = sum( tmp[,FR1] + 
-																			tmp[,CDR1] +
-																			tmp[,FR2] +
-																			tmp[,CDR2] +
-																			tmp[,FR3])
+		transitionTable[NT1,NT2] = sum( tmp[,CDR1] +
+																		tmp[,FR2] +
+																		tmp[,CDR2] +
+																		tmp[,FR3])
 	}
 }
 write.table(x=transitionTable, file="transitions.txt", sep=",",quote=F,row.names=T,col.names=NA)