getCentromereDistCounts: Get the breakpoint count per chromosome arm

In macintyrelab/CNpare: Comparing tumour copy number profiles

Get the breakpoint count per chromosome arm

Description

Helper function for extractCopynumberFeatures. Approach developed by Geoff Macintyre et al. 2018

Usage

getCentromereDistCounts(abs_profiles, centromeres, chrlen)

Arguments

abs_profiles	absolute copy-number profiles
centromeres	centromere positions
chrlen	chromosome length

Value

Matrix with breakpoint count per chromosome arm

Examples

profiles<-getProfiles(segcn=cells_segcn,
    samples=unique(cells_segcn$sample)[1:4])
gaps<-CNpare:::gaps
centromeres<-centromeres<-gaps[gaps[,8]=="centromere",]
bpchrarm<-getCentromereDistCounts(profiles,centromeres,CNpare:::chrlen)

macintyrelab/CNpare documentation built on April 15, 2022, 4:46 a.m.