prune_by_size: Remove segments smaller than the kit resolution.

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

Remove segments smaller than the kit resolution.

Description

Remove segments smaller than the kit resolution.

Usage

prune_by_size(segments, threshold = 300)

Arguments

segments	A GRanges object containing the segments, their copy number and copy number types.
threshold	Number indicating the minimum segment size to be kept (in kilobases). Defaults to the Oncoscan assay resolution outside of cancer genes: 300Kb.

Value

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

Examples

segs.300k <- prune_by_size(segs.chas_example)
segs.50k <- prune_by_size(segs.chas_example, 50)

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