getUnifiedMap: Merge adjacent break points

In CHAT: Clonal Heterogeneity Analysis Tool

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.

Details

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

Value

a vector containing the merged break point positions.

Author(s)

Bo Li

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)

CHAT documentation built on May 29, 2017, 10:32 p.m.