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 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. Other functions are available for visualization after PCoA, or to facilitate transfer of data between genlight/genind objects and newhybrids, related, phylip packages etc.


Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.


1.0 by Bernd Gruber, 2 months ago

Browse source code at

Authors: Bernd Gruber [aut, cre], Arthur Georges [aut], Peter J. Unmack [ctb], Oliver Berry [ctb]

Documentation:   PDF Manual  

GPL-2 license

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

Depends on adegenet

Suggests knitr, rmarkdown, mmod, PopGenReport

See at CRAN