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, 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.

Version: 1.0.5
Depends: R (≥ 3.1.1), adegenet (≥ 2.0.0)
Imports: plyr, tidyr, reshape2, MASS, ggplot2, directlabels, quadprog, rgl, misc3d, pca3d, utils, Demerelate, seqinr, pegas, SNPassoc, methods, doParallel, stats, data.table, parallel, foreach, stringr, ape, vegan, SNPRelate, StAMPP, dismo, DBI, qvalue, plotly, sp, rgdal
Suggests: knitr, rmarkdown, mmod, PopGenReport
Published: 2018-05-11
Author: Bernd Gruber [aut, cre], Arthur Georges [aut], Peter J. Unmack [ctb], Lindsay V. Clark [ctb], Oliver Berry [ctb]
Maintainer: Bernd Gruber <bernd.gruber at canberra.edu.au>
License: GPL-2
NeedsCompilation: no
CRAN checks: dartR results


Reference manual: dartR.pdf
Vignettes: dartR_Introduction
Package source: dartR_1.0.5.tar.gz
Windows binaries: r-devel: dartR_1.0.5.zip, r-release: dartR_1.0.5.zip, r-oldrel: dartR_1.0.5.zip
OS X binaries: r-release: dartR_1.0.5.tgz, r-oldrel: dartR_1.0.tgz
Old sources: dartR archive


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