gl.report.callrate

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

specify the type of report by locus (method="loc") or individual (method="ind") [default method="loc"]

method

specify if a histogram of call rate is to be produced [default TRUE]

plot

-- 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 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 reports the number of missing values for each
of several percentiles. The script gl.filter.callrate() will filter out the loci with call rates below a specified threshold.

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.

gl.report.callrate: Report summary of Call Rate for loci or individuals

Description

Usage

Arguments

Value

Examples