gl2plink

-- name of the genlight object containing the SNP data [required]

-- file name of the output file (including extension) [default plink.csv]

outfile

-- path where to save the output file [default tempdir(), mandated by CRAN]. Use outpath=getwd() when calling this function or set.tempdir &lt;- getwd() elsewhere in your script
to direct output files to your working directory.

outpath

-- verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]

verbose

This function exports a genlight object into PLINK format and save it into a file

Functions are provided that facilitate the import and analysis of
SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. The main focus is on data generated
by DarT (Diversity Arrays Technology). However, once SNP or related fragment
presence/absence data from any source is imported into a genlight object many
of the functions can be used. Functions are available for input and output of
SNP and silicodart data, for reporting on and filtering on various criteria
(e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency).
Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions
are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data
between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.

gl2plink: Converts a genlight object to PLINK file format

Description

Usage

Arguments

References

Examples