[Patchwork-commits] r134 - pkg/patchworkCG/R

[noreply at r-forge.r-project.org]

Author: mayrhofer
Date: 2012-06-25 13:53:55 +0200 (Mon, 25 Jun 2012)
New Revision: 134

Modified:
   pkg/patchworkCG/R/patchwork.CG.copynumbers.r
Log:
Updated CN calculation @ X and Y.

Modified: pkg/patchworkCG/R/patchwork.CG.copynumbers.r
===================================================================
--- pkg/patchworkCG/R/patchwork.CG.copynumbers.r	2012-06-04 13:17:56 UTC (rev 133)
+++ pkg/patchworkCG/R/patchwork.CG.copynumbers.r	2012-06-25 11:53:55 UTC (rev 134)
@@ -1,4 +1,4 @@
-patchwork.CG.copynumbers = function(cn2,delta,het,hom,maxCn=8,ceiling=1,name="copynumbers_",CGfile=NULL,forcedelta=F)
+patchwork.CG.copynumbers = function(cn2,delta,het,hom,maxCn=8,ceiling=1,name="copynumbers_",CGfile=NULL,forcedelta=F,male.sample=F,male2femref=T)
 	{
 	data(ideogram,package="patchworkCG")
 	
@@ -294,6 +294,35 @@
 	tumor_percentDNA <- xdelta / expected_delta
     tumor_percent <- tumor_percentDNA/(meanCn/2) / ( tumor_percentDNA/(meanCn/2) + (1-tumor_percentDNA) )
 
+    ## Fix sex chromosomes in case of male sample.
+    if (male.sample) {
+        ix <- which(!is.autosome(regions$chr))
+        regions$mCn[ix] <- 0
+        ## Treats differently depending on sex of the reference
+        if (!male2femref) {
+            # X and Y (originally cn1) were compared to cn1 (matched normal or male references).
+            # Unchanged copy number (=1) is expected at relative coverage 1. 
+            # Gains/loss are expected at xdelta (the delta of the autosomes)*2.
+            rawcopychange <- (regions$median[ix]-1) / (xdelta*2)
+            regions$Cn[ix] <- round(1+rawcopychange)
+            regions$fullCN[ix] <- paste('cn',round(1+rawcopychange),'m0')
+        } else 
+        {
+            # X and Y (originally cn1) were compared to cn2 (female references).
+            # Unchanged copy number (=1) is expected at relative coverage 1/2. 
+            # Gains/loss are expected at xdelta from there.
+            rawcopychange <- (regions$median[ix]-1/2) / (xdelta)
+            regions$Cn[ix] <- round(1+rawcopychange)
+            regions$fullCN[ix] <- paste('cn',round(1+rawcopychange),'m0')
+        }
+    }
+    ## And a small fix on female samples
+    if (!male.sample) {
+        ix <- which(regions$chr=='chrY')
+        regions$mCn[ix] <- regions$Cn[ix] <- 0
+    }
+
+
     regions$meanCn <- meanCn
     regions$tumor_percent <- tumor_percent