| read.VCF {hierfstat} | R Documentation |
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
Examples
filepath <-system.file("extdata", "LCT.vcf.gz", package="gaston")
x1 <- read.VCF( filepath )
x1
[Package hierfstat version 0.5-11 Index]