bedr (version 1.0.7)

vcf2bed: 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)

Value

A bed styled R object or an external file

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

Author

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)