merge_segments: Merge segments with respect to the kit resolution and the...

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

Merge segments with respect to the kit resolution and the copy number.

Description

Merge segments with respect to the kit resolution and the copy number.

Usage

merge_segments(segments, kit.resolution = 300)

Arguments

segments	A GRanges object containing the segments, their copy number and copy number types.
kit.resolution	Number >0 indicating the minimum segment size detectable by the technique (in kilobases). Defaults to the Oncoscan assay resolution outside of cancer genes: 300Kb.

Details

If two segments are at a distance smaller than the resolution, then the segments are merged if the share the same cn value. Note that the function does not look at the copy number type or subtype but only at the actual copy number to decide whether segments can be merged.

Value

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

Examples

segs.merged <- merge_segments(segs.chas_example)
segs.merged_50k <- merge_segments(segs.chas_example, 50)

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