callLOH: Get regions of LOH

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

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.