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.


Reference manual

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install.packages("dartR") by Bernd Gruber, 6 months ago

Browse source code at

Authors: Bernd Gruber [aut, cre] , Arthur Georges [aut] , Jose L. Mijangos [aut] , Peter J. Unmack [ctb] , Oliver Berry [ctb] , Lindsay V. Clark [ctb] , Floriaan Devloo-Delva [ctb]

Documentation:   PDF Manual  

GPL-2 license

Imports stats, methods, utils, plyr, tidyr, MASS, stringr, ape, vegan, SNPRelate, StAMPP, sp, PopGenReport, hierfstat, robustbase, gridExtra, HardyWeinberg, foreach, dplyr, crayon, devtools

Depends on adegenet, ggplot2

Suggests knitr, rmarkdown, rgl, parallel, doParallel, data.table, reshape2, pca3d, dismo, pegas, directlabels, rgdal, leaflet.minicharts, leaflet, rrBLUP, poppr, Rcpp, igraph, qvalue, gdistance, seqinr, pheatmap, RColorBrewer, gplots, vcfR, mmod, plotly, ggthemes, ggrepel, raster

See at CRAN