gl.keep.ind

-- name of the genlight object containing SNP genotypes or a genind object containing presence/absence data [required]

-- a list of individuals to be removed [required]

ind.list

-- Recalculate the locus metadata statistics [default FALSE]

recalc

-- Remove monomorphic loci [default TRUE]

mono.rm

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

The script, having deleted individuals, optionally identifies resultant monomorphic loci or loci
with all values missing and deletes them (using gl.filter.monomorphs.r). The script also optionally
recalculates statistics made redundant by the deletion of individuals from the dataset.

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.keep.ind: Remove all but the specified individuals from a genelight {adegenet} object

Description

Usage

Arguments

Value

Details

See Also

Examples