gl.rename.pop

Name of the genlight object containing SNP genotypes [required].

Name of population to be changed [required].

New name for the population [required].

Verbosity: 0, silent or fatal errors; 1, begin and end; 2,
progress log; 3, progress and results summary; 5, full report
 [default 2 or as specified using gl.set.verbosity].

verbose

Individuals are assigned to populations based on the specimen metadata data
file (csv) used with gl.read.dart().
This script renames a nominated population.
The script returns a genlight object with the new population name.

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.rename.pop: Renames a population in a genlight object

Description

Usage

Arguments

Value

Examples