cancerTiming (version 3.1.8)

mut2Seg: Align mutations to segments

Description

A function to match mutations into the segments that include them.

Usage

mut2Seg(mutData, segData, verbose = TRUE)

Arguments

mutData

matrix or data.frame. Column names must include `chr' and `position'

segData

matrix or data.frame. Column names must include `chr',`start',and `end' (in any order)

verbose

logical. If TRUE gives information about the progress and possible problems (e.g. if different chromosome names in the two sets )

Value

Details

This function finds which segments in the segData file contain the mutations and returns a data.frame with the concatenation of the mutation information and the segments information. The function relies on findOverlaps in the GenomicRanges package in bioconductor.

See Also

findOverlaps

Examples

if(require(GenomicRanges) & require(IRanges)){
	data(mutData)
	colnames(mutData)[1]<-c("chr")
	segs<-data.frame(chr=c(17,17),start=c(1,1.8e7+100),end=c(1.8e7,81195210),
		normCont=0.22,segId=c("CNLOH","Other"))
	##Trivial segmentation annotation for example
	mutId<-mut2Seg(mutData,segs)
	head(mutId)	
}