vcf2bed: convert a vcf to a bed file

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

convert a vcf to a bed file

Description

Convert a vcf to a bed file. Currently, it needs to read into R via read.vcf

Usage

vcf2bed(x, filename = NULL, header = FALSE, other = NULL, verbose = TRUE)

Arguments

x	a vcf object
filename	the name of file if you want it exported
header	indicate if the bed file has header or not when exported
other	fields to include apart from chr, start, end.
verbose	more words

Value

A bed styled R object or an external file

Author(s)

Daryl Waggott

Examples

clinVar.vcf.example <- system.file("extdata/clinvar_dbSNP138_example.vcf.gz", package = "bedr")
x <- read.vcf(clinVar.vcf.example)
x.bed <- vcf2bed(x)

bedr documentation built on April 11, 2025, 5:52 p.m.