CHAT (version 1.1)

getUnifiedMap: Merge adjacent break points

Description

Two sets of break points from one chromosome, typically from B-allele frequency and logR ratios respectively are inputs, and this function uses input from LRR as template to adjust break point positions in BAF if they are close enough to one of the LRR break points.

Usage

getUnifiedMap(seg.L.chr, seg.B.chr, map.chr, thr = 5)

Arguments

seg.L.chr

break point positions from LRR segmentation.

seg.B.chr

break point positions from BAF segmentation.

map.chr

SNP positions or starting position of aCGH markers.

thr

if two break points are located within thr number of markers, they will be merged.

Value

a vector containing the merged break point positions.

Details

Each set of break points contains even number, increasing integers, alternating between start and end positions of a DNA segment.

Examples

seg.L<-c(1,10,11,100,101,120)
seg.B<-c(1,11,12,60,61,120)
map.chr<-1:130
getUnifiedMap(seg.L,seg.B,map.chr)