Lfmm: Convert VCF to LFMM format

In nspope/r2vcftools: An R interface for vcftools

Description

Given a "vcfLink" object, converts the VCF file to the format used by LFMM in package LEA. Involves intermediate creation of a genotype matrix, so only biallelic SNPs are retained.

Usage

Lfmm(object, ...)

## S4 method for signature 'vcfLink'
Lfmm(object, output.file, verbose = TRUE)

Arguments

object	an object of class "vcfLink"
output.file	the filename to save the LFMM file to
verbose	print stdout from vcftools?

nspope/r2vcftools documentation built on Oct. 10, 2019, 2:06 a.m.