score_estwgd: Estimates the number of whole-genome doubling events (WGD).

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

Estimates the number of whole-genome doubling events (WGD).

Description

Estimates the number of whole-genome doubling events (WGD).

Usage

score_estwgd(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

Based on the publication from Carter et al. (Nature Biotechnology 2012; PubMed ID: 22544022). On a pan-cancer cohort, they observed that tumors that underwent one whole-genome doubling event had a ploidy (average copy number) between 2.2 and 3.4. This function relies on the function score_avgcn to compute the ploidy.

Value

A named list with two values: WGD (whole-genome doubling events) and avgCN (the average copy number). WGD values are 0 for no WGD event, 1 for one WGD event, 2 for several WGD events.

Examples

score_estwgd(segs.chas_example, oncoscan_na33.cov)

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