gl.filter.repavg

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

-- threshold value below which loci will be removed [default 0.99]

threshold

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

SNP datasets generated by DArT have in index, RepAvg, generated by reproducing the data independently for 30% of loci.
RepAvg is the proportion of alleles that give a repeatable result, averaged over both alleles for each locus.

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.filter.repavg: Filter loci in a genlight {adegenet} object based on average repeatability of alleles at a locus

Description

Usage

Arguments

Value

Examples