score_loh | R Documentation |
Compute the number HR deficiency-associated LOH regions.
score_loh(segments, arms.loh, arms.hetloss, kit.coverage)
segments |
A |
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 |
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).
An integer representing the number of HRD-LOH regions.
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)
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