adding gap expansion

Author: chrisamiller

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: copyCat
 Title: Find regions of genomic copy number loss and gain from short reads
-Version: 1.6.11
+Version: 1.6.12
 Author: Chris Miller
 Description: Uses the depth of short reads in windows across the genome to 
 	     identify regions of genomic copy-number gain and loss
 Maintainer: Chris Miller <[email protected]>
 LazyLoad: yes
 License: Apache License 2.0 | file LICENSE
 Depends: methods, foreach, doMC, IRanges, DNAcopy, stringr
-Packaged: 2016-11-30 12:45:10 PM; cmiller
+Packaged: 2017-04-18 02:55:38 PM; cmiller

R/cnSegments.R

@@ -237,7 +237,7 @@ trimSegmentEnds <- function(segs,rdo){
 ##-----------------------------------------------
 ## remove segments that overlap at least n% with a reference assembly gap
 ##
-removeGapSpanningSegments <- function(segs,rdo,maxOverlap=0.75){
+removeGapSpanningSegments <- function(segs,rdo,maxOverlap=0.75,gapExpansion=1.0){
   count = length(segs[,1]);
 
   if(!(file.exists(paste(rdo@params$annotationDirectory,"/gaps.bed",sep="")))){
@@ -247,7 +247,17 @@ removeGapSpanningSegments <- function(segs,rdo,maxOverlap=0.75){
   }
 
   gaps = read.table(paste(rdo@params$annotationDirectory,"/gaps.bed",sep=""))
-
+  #expand gaps if necessary
+  if(gapExpansion!=1){
+    print(paste("Using gap expansion of ",gapExpansion))
+    sizes=gaps[,3]-gaps[,2]
+    exp=round(((sizes*gapExpansion)-sizes)/2)
+    gaps[,2] = gaps[,2]-exp
+    gaps[,3] = gaps[,3]+exp
+    gaps[(gaps[,2]<0),2]=0 #no negative coords    exp=round(((sizes*gapExpansion)-sizes)/2)
+  }
+  
+  
   #intersect each chromosome separately
   newsegs = foreach(chr=names(rdo@chrs), .combine="rbind") %do%{
 

R/zzz.R

@@ -19,5 +19,5 @@
   sillyname(methods)
 
   initRdClass()
-  packageStartupMessage("Using copyCat version 1.6.11")
+  packageStartupMessage("Using copyCat version 1.6.12")
 }

man/removeGapSpanningSegments.Rd

@@ -10,7 +10,7 @@
   false-positive calls.
 }
 \usage{
-  removeGapSpanningSegments(segs,rdo,maxOverlap=0.75)
+  removeGapSpanningSegments(segs,rdo,maxOverlap=0.75,gapExpansion=1.0)
 }
 
 \arguments{
@@ -26,6 +26,10 @@
   \item{maxOverlap}{
     if a segment overlaps at least this much with a gap, it will be removed.
   }
+  \item{gapExpansion}{
+    expand each gap feature by this fraction before doing gap
+  filtering. A value of 1.3 would expand each gap by 30%.
+  }
 }
 \value{
   returns a dataframe with 5 columns: