gl.recalc.metrics

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

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

When individuals are deleted from a genlight object generated by DArT, the locus metrics no longer
apply. For example, the Call Rate may be different considering the subset of individuals, compared
with the full set. This script recalculates those affected locus metrics, namely, avgPIC, CallRate,
freqHets, freqHomRef, freqHomSnp, OneRatioRef, OneRatioSnp, PICRef and PICSnp. Metrics that remain
unaltered are RepAvg and TrimmedSeq as they are unaffected by the removal of individuals.

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

Importing and Analysing SNP and Silicodart Data Generated by
Genome-Wide Restriction Fragment Analysis

gl.recalc.metrics: Recalculate locus metrics when individuals or populations are deleted from a genlight {adegenet} object

Description

Usage

Arguments

Value

Details

See Also

Examples