gl.subsample.loci

-- name of the genlight object containing the SNP genotypes by specimen and population [required]

-- number of loci to include in the subsample [required]

-- "random", in which case the loci are sampled at random; or avgPIC, in which case the top n loci
ranked on information content (AvgPIC) are chosen [default "random"]

method

This is a support script, to subsample a genlight {adegenet} object based on loci. Two methods are used
to subsample, random and based on information content (avgPIC)

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.

Bernd Gruber

dartR

gl.subsample.loci: Subsample n loci from a genlight object and return as a genlight object

Description

Usage

Arguments

Value

Examples