dartR:Importing and Analysing 'SNP' and 'Silicodart' Data Generated by
Genome-Wide Restriction Fragment Analysis
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,
data from other sequencing platforms can be used once 'SNP' or
related fragment presence/absence data from any source is
imported. Genetic datasets are stored in a derived 'genlight'
format (package 'adegenet'), that allows for a very compact
storage of data and metadata. Functions are available for
importing and exporting of 'SNP' and 'silicodart' data, for
reporting on and filtering on various criteria (e.g.
'CallRate', heterozygosity, reproducibility, maximum allele
frequency). Additional functions are available for
visualization (e.g. Principle Coordinate Analysis) and creating
a spatial representation using maps. 'dartR' supports also the
analysis of 3rd party software package such as 'newhybrid',
'structure', 'NeEstimator' and 'blast'. Since version 2.0.3 we
also implemented simulation functions, that allow to forward
simulate 'SNP' dynamics under different population and
evolutionary dynamics. Comprehensive tutorials and support can
be found at our 'github' repository:
github.com/green-striped-gecko/dartR/. If you want to cite
'dartR', you find the information by typing citation('dartR')
in the console.
