Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Facilitates 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.base' is the 'base' package of the 'dartRverse' suits of packages. To install the other packages, we recommend to install the 'dartRverse' package, that supports the installation of all packages in the 'dartRverse'. If you want to cite 'dartR', you find the information by typing citation('dartR.base') in the console.


Reference manual

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install.packages("dartR.base")

1.2.3 by Bernd Gruber, 7 months ago


https://green-striped-gecko.github.io/dartR/


Report a bug at https://groups.google.com/g/dartr?pli=1


Browse source code at https://github.com/cran/dartR.base


Authors: Bernd Gruber [aut, cre] , Arthur Georges [aut] , Jose L. Mijangos [aut] , Carlo Pacioni [aut] , Diana Robledo-Ruiz [aut] , Peter J. Unmack [ctb] , Oliver Berry [ctb] , Lindsay V. Clark [ctb] , Emily Stringer [ctb] , Floriaan Devloo-Delva [ctb] , Eric Archer [ctb] , Ching Ching Lau [ctb]


Documentation:   PDF Manual  


GPL (>= 3) license


Imports ape, crayon, data.table, foreach, gridExtra, methods, patchwork, plyr, reshape2, SNPRelate, StAMPP, stats, stringr, tidyr, utils, MASS, bigstatsr, bigsnpr, snpStats, gtools

Depends on ggplot2, dplyr, dartR.data, adegenet

Suggests boot, devtools, directlabels, dismo, doParallel, expm, gdistance, gganimate, ggrepel, grid, gtable, ggthemes, gplots, HardyWeinberg, hierfstat, igraph, iterpc, knitr, label.switching, lattice, leaflet, leaflet.minicharts, markdown, mmod, networkD3, parallel, pegas, pheatmap, plotly, poppr, proxy, purrr, qvalue, RColorBrewer, Rcpp, rgl, rmarkdown, rrBLUP, scales, seqinr, sf, shinyBS, shinyjs, shinythemes, shinyWidgets, SIBER, stringi, tibble, vcfR, zoo, viridis, fields, testthat, ggtern, dendextend, ggdendro, terra, R.utils


Depended on by dartR.captive, dartR.popgen, dartR.sexlinked, dartR.sim, dartR.spatial.

Suggested by dartRverse.


See at CRAN