score_td: Compute the number of large tandem duplication (TDplus).

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

Compute the number of large tandem duplication (TDplus).

Description

Compute the number of large tandem duplication (TDplus).

Usage

score_td(segments)

Arguments

segments

A GRanges object containing the segments, their copy number and copy number types.

Details

Procedure based on the paper from Popova et al., Cancer Res 2016 (PMID: 26787835). The TDplus score is defined as the number of regions larger than 1Mb but smaller or equal to 10Mb with a gain of one or two copies. This score was linked to CDK12-deficient tumors. They also identified as second category of tandem duplication whose size is smaller or equal than 1Mb and around 300Kb but could not link it to a phenotype. Note that due to its resolution the Oncoscan assay will most likely miss this second category. Nonetheless it is reported by the function.

Value

A list of integer containing the TDplus score ('TDplus') and the small TD score ('TD').

Examples

score_td(segs.chas_example)

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