Mercurial > repos > davidvanzessen > mutation_analysis

changeset 71:9165bec41c02 draft

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Uploaded
author davidvanzessen
date Wed, 04 May 2016 03:48:57 -0400
parents c2e1d5a93f98
children 51d92233fb5d
files mutation_analysis.r
diffstat 1 files changed, 21 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/mutation_analysis.r	Thu Apr 28 08:11:55 2016 -0400
+++ b/mutation_analysis.r	Wed May 04 03:48:57 2016 -0400
@@ -51,6 +51,7 @@
                     "CDR2.IMGT.Nb.of.nucleotides",
                     "FR2.IMGT.a.t",
                     "CDR1.IMGT.Nb.of.mutations",
+                    "CDR3.IMGT.Nb.of.nucleotides",
                     "CDR1.IMGT.a.g",
                     "FR3.IMGT.a.c",
                     "FR1.IMGT.g.a",
@@ -222,6 +223,16 @@
 	  matrx[9,x] = round(f(tmp$nonSilentMutationsCDR, na.rm=T), digits=1)
 	  matrx[9,y] = round(f(tmp$silentMutationsCDR, na.rm=T), digits=1)
 	  matrx[9,z] = round(matrx[9,x] / matrx[9,y], digits=1)
+	  
+	  if(fname == "sum"){
+		  matrx[10,x] = round(f(rowSums(tmp[,c("FR2.IMGT.Nb.of.nucleotides", "FR3.IMGT.Nb.of.nucleotides")], na.rm=T)), digits=1)
+		  matrx[10,y] = round(f(tmp$VRegionNucleotides, na.rm=T), digits=1)
+		  matrx[10,z] = round(matrx[10,x] / matrx[10,y], digits=1)
+		  
+		  matrx[11,x] = round(f(rowSums(tmp[,c("CDR1.IMGT.Nb.of.nucleotides", "CDR3.IMGT.Nb.of.nucleotides")], na.rm=T)), digits=1)
+		  matrx[11,y] = round(f(tmp$VRegionNucleotides, na.rm=T), digits=1)
+		  matrx[11,z] = round(matrx[11,x] / matrx[11,y], digits=1)
+	  }
   }
   
   transitionTable = data.frame(A=zeros,C=zeros,G=zeros,T=zeros)
@@ -275,7 +286,11 @@
 	func = funcs[[i]]
 	fname = fnames[[i]]
 	
-	matrx = matrix(data = 0, ncol=((length(genes) + 1) * 3),nrow=9)
+	rows = 9
+	if(fname == "sum"){
+		rows = 11
+	}
+	matrx = matrix(data = 0, ncol=((length(genes) + 1) * 3),nrow=rows)
 
 	for(i in 1:length(genes)){
 	  matrx = calculate_result(i, genes[i], dat, matrx, func, fname, genes[i])
@@ -284,7 +299,11 @@
 	matrx = calculate_result(i + 1, ".*", dat, matrx, func, fname, name="all")
 	
 	result = data.frame(matrx)
-	row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C G (%)", "Transitions at A T (%)", "Targeting of A T (%)", "FR R/S (ratio)", "CDR R/S (ratio)")
+	if(fname == "sum"){
+		row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C G (%)", "Transitions at A T (%)", "Targeting of A T (%)", "FR R/S (ratio)", "CDR R/S (ratio)", "nt in FR", "nt in CDR")
+	} else {
+		row.names(result) = c("Number of Mutations (%)", "Transition (%)", "Transversions (%)", "Transitions at G C (%)", "Targeting of C G (%)", "Transitions at A T (%)", "Targeting of A T (%)", "FR R/S (ratio)", "CDR R/S (ratio)")
+	}
 
 	write.table(x=result, file=paste("mutations_", fname, ".txt", sep=""), sep=",",quote=F,row.names=T,col.names=F)
 }