score_lst: Compute the number of Large-scale State Transitions (LSTs).

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

Compute the number of Large-scale State Transitions (LSTs).

Description

Compute the number of Large-scale State Transitions (LSTs).

Usage

score_lst(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

Procedure based on the paper from Popova et al, Can. Res. 2012 (PMID: 22933060). First segments smaller than 3Mb are removed, then segments are smoothed with respect to copy number at a distance of 3Mb. The number of LSTs is the number of breakpoints (breakpoints closer than 3Mb are merged) that have a segment larger or equal to 10Mb on each side. This score was linked to BRCA1/2-deficient tumors.

Value

An integer representing the number of LSTs.

Examples

score_lst(segs.chas_example, oncoscan_na33.cov)

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