[Patchwork-commits] r135 - pkg/patchworkCG/R

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

Author: mayrhofer
Date: 2012-06-25 14:49:40 +0200 (Mon, 25 Jun 2012)
New Revision: 135

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	2012-06-25 11:53:55 UTC (rev 134)
+++ pkg/patchworkCG/R/patchwork.CG.copynumbers.r	2012-06-25 12:49:40 UTC (rev 135)
@@ -1,4 +1,4 @@
-patchwork.CG.copynumbers = function(cn2,delta,het,hom,maxCn=8,ceiling=1,name="copynumbers_",CGfile=NULL,forcedelta=F,male.sample=F,male2femref=T)
+patchwork.CG.copynumbers = function(cn2,delta,het,hom,maxCn=8,ceiling=1,name="copynumbers_",CGfile=NULL,forcedelta=F)
 	{
 	data(ideogram,package="patchworkCG")
 	
@@ -294,33 +294,33 @@
 	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$Cn[ix] <- 0
-    }
+    # ## Fix sex chromosomes in case of male sample.
+    # if (male.sample) {
+    #     ix <- which(!is.autosome(regions$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