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: |
2.0.4 |
| Depends: |
R (≥ 3.5), adegenet (≥ 2.0.0), ggplot2, dplyr |
| Imports: |
ape, crayon, data.table, fields, foreach, gridExtra, MASS, methods, patchwork, plyr, PopGenReport, raster, reshape2, shiny, SNPRelate, sp, StAMPP, stats, stringr, tidyr, utils, vegan |
| Suggests: |
boot, devtools, directlabels, dismo, doParallel, expm, gdistance, gganimate, ggrepel, ggtern, ggthemes, gplots, HardyWeinberg, hierfstat, igraph, iterpc, knitr, label.switching, leaflet, leaflet.minicharts, markdown, mmod, networkD3, parallel, pca3d, pegas, pheatmap, plotly, poppr, proxy, purrr, qvalue, RColorBrewer, Rcpp, rgl, rmarkdown, rrBLUP, scales, seqinr, shinyBS, shinyjs, shinythemes, shinyWidgets, SIBER, snpStats, stringi, terra, tibble, tidyverse, vcfR |
| Published: |
2022-06-05 |
| Author: |
Bernd Gruber [aut, cre],
Arthur Georges [aut],
Jose L. Mijangos [aut],
Carlo Pacioni [aut],
Peter J. Unmack [ctb],
Oliver Berry [ctb],
Lindsay V. Clark [ctb],
Floriaan Devloo-Delva [ctb],
Eric Archer [ctb] |
| Maintainer: |
Bernd Gruber <bernd.gruber at canberra.edu.au> |
| License: |
GPL (≥ 3) |
| NeedsCompilation: |
no |
| Citation: |
dartR citation info |
| CRAN checks: |
dartR results |