score_avgcn: Compute the average copy number variation across the genome.

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

Compute the average copy number variation across the genome.

Description

Compute the average copy number variation across the genome.

Usage

score_avgcn(segments, kit.coverage)

Arguments

segments	A GRanges object containing the segments, their copy number and copy number types.
kit.coverage	A GRanges object containing the regions covered on each chromosome arm.

Details

Compute the weighted average (by segment length) of the copy number variation. LOH segments and sexual chromosomes are excluded. Copy number variation is rounded to the next level (1.67 -> 1 but 2.33 -> 3).

Value

A decimal value

Examples

score_avgcn(segs.chas_example, oncoscan_na33.cov)

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