utils.recalc.avgpic

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

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

The locus metadata supplied by DArT has OneRatioRef, OneRatioSnp, PICRef,	PICSnp, and	AvgPIC included,
but the allelec composition will change when some individuals are removed from the dataset and so the initial statistics will
no longer apply. This script recalculates these statistics and places the recalculated values in the appropriate place 
in the genlight object.

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

Arthur Georges

Peter J. Unmack

Lindsay V. Clark

Oliver Berry

utils.recalc.avgpic function

A utility script to recalculate the OneRatioRef, OneRatioSnp, PICRef,	PICSnp, and	AvgPIC by locus after some 
populations have been deleted. — utils.recalc.avgpic

utils.recalc.avgpic: A utility script to recalculate the OneRatioRef, OneRatioSnp, PICRef, PICSnp, and AvgPIC by locus after some populations have been deleted.

Description

Usage

Arguments

Value

Details

Examples