get_oncoscan_coverage_from_bed: Load the oncoscan coverage BED file into a GenomicRanges...
In yannchristinat/oncoscanR: Secondary analyses of CNV data (HRD and more)

get_oncoscan_coverage_from_bed

R Documentation

Load the oncoscan coverage BED file into a GenomicRanges object.

Description

Load the oncoscan coverage BED file into a GenomicRanges object.

Usage

get_oncoscan_coverage_from_bed(filename)

Arguments

filename

Path to the coverage BED file.

Details

Expects the following columns from the BED file (no header): 1. Name of the chromosomal arm (e.g. "1p") 2. Start position of the arm 3. End position of the arm

Value

A GRanges object containing the regions covered on each chromosome arm.

Examples

oncoscan_na33.cov <- get_oncoscan_coverage_from_bed(
       system.file('extdata', 'Oncoscan.na33.r2.cov.processed.bed',
       package = 'oncoscanR'))

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