gl.read.vcf: Converts a vcf file into a genlight object

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Converts a vcf file into a genlight object

Description

This function needs package vcfR, please install it. The converted genlight object does not have individual metrics. You need to add them 'manually' to the other$ind.metrics slot.

Usage

gl.read.vcf(vcffile, verbose = NULL)

Arguments

vcffile	A vcf file (works only for diploid data) [required].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].

Value

A genlight object.

Author(s)

Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)

Examples

## Not run: 
obj <- gl.read.vcf(system.file('extdata/test.vcf', package='dartR'))

## End(Not run)

green-striped-gecko/dartR documentation built on Jan. 31, 2024, 10:14 a.m.