callLOH: Get regions of LOH

View source: R/callLOH.R

callLOHR Documentation

Get regions of LOH

Description

This function provides detailed LOH information by region.

Usage

callLOH(res, id = 1, arm.cutoff = 0.9, keep.no.snp.segments = TRUE)

Arguments

res

Return object of the runAbsoluteCN function.

id

Candidate solution to extract LOH from. id=1 will use the maximum likelihood solution.

arm.cutoff

Min fraction LOH on a chromosome arm to call whole arm events.

keep.no.snp.segments

Segments without heterozygous SNPs have no LOH information. This defines whether these segments should be reported anyways.

Value

Returns data.frame with LOH regions.

Author(s)

Markus Riester

See Also

runAbsoluteCN

Examples


data(purecn.example.output)
head(callLOH(purecn.example.output))


lima1/PureCN documentation built on Sept. 17, 2024, 5:48 a.m.