gl.filter.callrate

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

-- "loc" to specify that loci are to be filtered, "ind" to specify that specimens are to be filtered [default "loc"]

method

-- threshold value below which loci will be removed [default 0.95]

threshold

SNP datasets generated by DArT have missing values primarily arising from failure to call a SNP because of a mutation
at one or both of the the restriction enzyme recognition sites. This script filters out loci (or specimens) for which the call rate is
lower than a specified value. The script will also filter out loci (or specimens) in SilicoDArT (presence/absence) datasets where the call rate
is lower than the specified value. In this case, the data are missing owing to low coverage.

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.

Bernd Gruber

gl.filter.callrate: Filter loci or specimens in a genlight {adegenet} object based on call rate

Description

Usage

Arguments

Value

Examples