[Patchwork-commits] r104 - pkg/patchworkCG/R

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

Author: sebastian_d
Date: 2012-02-29 11:29:39 +0100 (Wed, 29 Feb 2012)
New Revision: 104

Modified:
   pkg/patchworkCG/R/patchwork.CG.r
   pkg/patchworkCG/R/patchwork.CGCNV.r
Log:
changed segs to segm in patchwork.CGCNV

Modified: pkg/patchworkCG/R/patchwork.CG.r
===================================================================
--- pkg/patchworkCG/R/patchwork.CG.r	2012-02-27 12:54:13 UTC (rev 103)
+++ pkg/patchworkCG/R/patchwork.CG.r	2012-02-29 10:29:39 UTC (rev 104)
@@ -274,8 +274,8 @@
 	#------------------------------------------------#
 	# Plot
 	#------------------------------------------------#
+	#patchwork.CGCNV(cn2=0.75,delta=0.36,het=0.5,hom=0.97) #HCC1187
 	
-	
 	cat("Initiating Plotting \n")
 	CG_karyotype(segm$chr,segm$start,segm$end,segm$ratio,segm$ai,
 					name=name,xlim=c(0,2.4),ylim=c(0,1))

Modified: pkg/patchworkCG/R/patchwork.CGCNV.r
===================================================================
--- pkg/patchworkCG/R/patchwork.CGCNV.r	2012-02-27 12:54:13 UTC (rev 103)
+++ pkg/patchworkCG/R/patchwork.CGCNV.r	2012-02-29 10:29:39 UTC (rev 104)
@@ -16,7 +16,7 @@
     tix=NULL     #temporary index
     int=NULL     ## contains coverage estimate of each (total) copy number
     ai=NULL         ## contains Allelic Imbalance Ratio estimate of each copy number variant.
-    regions <- segs
+    regions <- segm
     regions$np <- round((regions$end - regions$start)/10000)
     regions <- regions[(is.autosome(regions$chr)&regions$np>50)&(!is.nan(regions$ai)),] ## will use these regions
     regions <- regions[!is.na(regions$ratio),]
@@ -216,7 +216,7 @@
 
 	## Reassignment of regions! This removes regions$np which is used later..
 	##  Assign total and minor copy numbers to all segments.
-    regions <- segs[!is.na(segs$ratio),]    ## This time, work on all segments available.
+    regions <- segm[!is.na(segm$ratio),]    ## This time, work on all segments available.
     regions$np <- round((regions$end - regions$start)/10000)
 
     Cn <- NULL            ## Total copy number