score_gloh: Compute the genomic LOH score.

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

Compute the genomic LOH score.

Description

Compute the genomic LOH score.

Usage

score_gloh(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 loss.
kit.coverage	A GRanges object containing the regions covered on each chromosome arm.

Details

The percentage genomic LOH score is computed as described in the FoundationFocus CDx BRCA LOH assay; i.e. the percentage of bases covered by the Oncoscan that display a loss of heterozygosity independently of the number of copies, excluding chromosomal arms that have a global LOH (>=90 arm length). To compute with the armlevel_alt function on LOH segments only). This score was linked to BRCA1/2-deficient tumors.

Value

An integer representing the percentage of LOH bases.

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_gloh(segs.chas_example, names(armlevel.loh), names(armlevel.hetloss),
oncoscan_na33.cov)

yannchristinat/oncoscanR documentation built on Oct. 26, 2024, 12:58 p.m.