score_gloh | R Documentation |
Compute the genomic LOH score.
score_gloh(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 loss. |
kit.coverage |
A |
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.
An integer representing the percentage of LOH bases.
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)
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