read.VCF: Reads a VCF file into a BED object

In hierfstat: Estimation and Tests of Hierarchical F-Statistics

Reads a VCF file into a BED object

Description

Reads a https://samtools.github.io/hts-specs/Variant Call Format (VCF) file into a BED object, retaining bi-allelic SNPs only

Usage

read.VCF(fname,BiAllelic=TRUE,...)

Arguments

fname	VCF file name. The VCF file can be compressed (VCF.gz)
BiAllelic	Logical. If TRUE, only bi-allelic SNPs are retained, otherwise, all variant are kept
...	other arguments to pass to the function

Value

A bed.matrix-class object

See Also

read.vcf

Examples

 
 filepath <-system.file("extdata", "LCT.vcf.gz", package="gaston")
 x1 <- read.VCF( filepath )
 x1

hierfstat documentation built on May 6, 2022, 1:05 a.m.