score_loh: Compute the number HR deficiency-associated LOH regions.

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

Compute the number HR deficiency-associated LOH regions.

Description

Compute the number HR deficiency-associated LOH regions.

Usage

score_loh(segments, arms.loh, arms.hetloss, kit.coverage)

Arguments

segments	A GRanges object containing the segments, their copy number and copy number types.
arms.loh	A list of arms with global/arm-level LOH alteration.
arms.hetloss	A list of arms with global/arm-level heterozygous losses.
kit.coverage	A GRanges object containing the regions covered on each chromosome arm.

Details

Procedure based on the paper from Abkevich et al., Br J Cancer 2012 (PMID: 23047548). All LOH segments larger than 15Mb but excluding chromosome with a global LOH alteration (to compute with the armlevel_alt function on LOH segments only). This score was linked to BRCA1/2-deficient tumors. Note that the function will merge overlapping or neighbor LOH segments (at a distance of 1bp).

Value

An integer representing the number of HRD-LOH regions.

Examples

armlevel.loh <- armlevel_alt(get_loh_segments(segs.chas_example),
                             kit.coverage = oncoscan_na33.cov)
armlevel.hetloss <- armlevel_alt(get_hetloss_segments(segs.chas_example),
                             kit.coverage = oncoscan_na33.cov)
score_loh(segs.chas_example, names(armlevel.loh), names(armlevel.hetloss),
oncoscan_na33.cov)

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