gaston (version 1.4.9)

read.vcf: Create a bed.matrix from VCF files

Description

Create a bed.matrix from a .vcf file.

Usage

read.vcf(filename, max.snps, verbose = getOption("gaston.verbose",TRUE))

Arguments

filename

Name of VCF file

max.snps

The maximal number of SNPs to read.

verbose

If TRUE, display information on the function progress

Value

bed.matrix

Details

This function relies on the package WhopGenome. Details about vcf format are given in http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

See Also

read.bed.matrix

Examples

# Read vcf file
filepath <-system.file("extdata", "LCT.vcf.gz", package="gaston")
x <- read.vcf( filepath )
x