load_ascat: Load am ASCAT text export file.

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

Load am ASCAT text export file.

Description

Load am ASCAT text export file.

Usage

load_ascat(filename, kit.coverage)

Arguments

filename	Path to the ASCAT file.
kit.coverage	A GRanges object containing the regions covered on each chromosome arm by the kit.

Details

The ASCAT file is expected to have the following column names: 'chr' (chromosome number), 'startpos' (first position of CNV segment), 'endpos' (last position of CNV segment), 'nMajor' (Number of copies of the major allele) and 'nMinor' (Number of copies of the minor allele).

The segments are attributed to each chromosome arm and split if necessary.

Value

A GRanges object containing the segments, their copy number (field cn), their copy number types (field cntype). cntype contains either 'Gain', 'Loss' or 'LOH'. If the file contains twice the same segment or does not respect the format specifications, then an error is raised. NB. If the chromosome name is in the format '1' and not 'chr1' and will be transformed if needed.

Examples

segs.filename <- system.file('extdata', 'ascat_example.txt',
  package = 'oncoscanR')
segs.ascat_example <- load_ascat(segs.filename, oncoscan_na33.cov)

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