gl.merge.pop

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

A list of populations to be merged [required].

Name of the new 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 assigns individuals from two nominated populations into a new
single population. It can also be used to rename populations.
The script returns a genlight object with the new population assignments.

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.merge.pop: Merges two or more populations in a genlight object into one population

Description

Usage

Arguments

Value

Examples