vcf2bed: convert a vcf to a bed file

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

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)

Example output

sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied


######################
#### bedr v1.0.3 ####
######################

checking binary availability...
  * Checking path for bedtools... FAIL
  * Checking path for bedops... FAIL
  * Checking path for tabix... FAIL
tests and examples will be skipped on R CMD check if binaries are missing

READING VCF
 * checking if file exists... PASS
 * Reading vcf header...
   Done
 * Reading vcf body...
   Done
 * Parse vcf header...
   Done
CONVERT VCF TO BED
There were 12 warnings (use warnings() to see them)

bedr documentation built on May 2, 2019, 11:36 a.m.