gl.filter.dups

<p>-- name of the genlight object containing the SNP data, or the genind object containing the SilocoDArT data [required]</p>

<p>SNP datasets generated by DArT include fragments with more than one SNP and record them separately with the same CloneID (=AlleleID).
These multiple SNP loci within a fragment are likely to be linked, and so you may wish to remove duplicates.
This script filters out duplicate loci after ordering the genlight object on based on reproducibility, PIC in that order.</p>

Functions are provided that facilitate the import and analysis of
snp 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. Other functions
are available for visualization after PCoA, or to facilitate transfer of data
between genlight/genind objects and newhybrids, related, phylip packages etc.

gl.filter.dups: Filter duplicated loci in a genlight {adegenet} object

Description

Usage

Arguments

Value

Examples