importBed: Read bed-file into GRanges

In ataudt/aneufinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Read bed-file into GRanges

Description

This is a simple convenience function to read a bed(.gz)-file into a GRanges-class object. The bed-file is expected to have the following fields: chromosome, start, end, name, score, strand.

Usage

importBed(bedfile, skip = 0, chromosome.format = "NCBI")

Arguments

bedfile	Filename of the bed or bed.gz file.
skip	Number of lines to skip at the beginning.
chromosome.format	Desired format of the chromosomes. Either 'NCBI' for (1,2,3 ...) or 'UCSC' for (chr1,chr2,chr3 ...).

Value

A GRanges-class object with the contents of the bed-file.

Author(s)

Aaron Taudt

Examples

## Get an example BED file with single-cell-sequencing reads
bedfile <- system.file("extdata", "KK150311_VI_07.bam.bed.gz", package="AneuFinderData")
## Import the file and skip the first 10 lines
data <- importBed(bedfile, skip=10)

ataudt/aneufinder documentation built on April 18, 2023, 4:20 a.m.