map_noisy_segments: Map all segments within an interval to the dominant CN state

In lculibrk/Ploidetect: Ploidetect - Detection of tumour purity, aneuploidy, and copy number variation from whole genome sequnce data

Map all segments within an interval to the dominant CN state

Description

map_noisy_segments takes in a genomic region on chromosome chr between start_pos and end_pos and produces a named list of vectors to be passed to curate_segments indicating a mapping between each segment and the most common segment in the region

Usage

map_noisy_segments(cna, chrom, start_pos, end_pos)

Arguments

cna	a data.table containing the bin-level copy number calls
chrom	the chromosome of interest
start_pos	the start position of the mapping
end_pos	the end position of the mapping - the segments of interest must have end <= this number

Value

a named list

lculibrk/Ploidetect documentation built on May 18, 2023, 5:53 p.m.