armlevel_alt: Get all globally-altered chromosome arms.

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

Get all globally-altered chromosome arms.

Description

Get all globally-altered chromosome arms.

Usage

armlevel_alt(segments, kit.coverage, threshold = 0.9)

Arguments

segments	A GRanges object containing the segments.
kit.coverage	A GRanges object containing the regions covered on each chromosome arm.
threshold	The minimum percentage of the arm to be considered as globally altered. Defaults to 80%.

Details

By default uses the sum of all alterations and set the arm as globally altered if \>80% of the arm is altered. Does not account for alteration type and copy number. Will run the function trim_to_coverage on the segments.

Value

A list of globally-altered chromosome arms with the percentage of arm altered.

Examples

arms <- armlevel_alt(segs.chas_example, oncoscan_na33.cov, 0.9)

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