adjust_loh: Trim LOH segments with respect to loss segments.

In yannchristinat/oncoscanR: Secondary analyses of CNV data (HRD and more)

Trim LOH segments with respect to loss segments.

Description

Trim LOH segments with respect to loss segments.

Usage

adjust_loh(segments)

Arguments

segments

A GRanges object containing the segments, their copy number and copy number types.

Details

LOH segments completely contained within (or equal to) a copy loss segment are deleted. LOH segments partially overlapping (on one end only) with a copy loss segment are trimmed to remove the overlap or split into several segments.

Value

A GRanges object containing the cleaned segments, their copy number and copy number types.

Examples

segs.adj <- adjust_loh(segs.chas_example)

yannchristinat/oncoscanR documentation built on Oct. 27, 2023, 11:19 p.m.