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.

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Description file content

Package
dartR
Type
Package
Title
Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis
Version
1.0.5
Date
2018-05-11
Description
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.
VignetteBuilder
knitr
Depends
R (>= 3.1.1), adegenet (>= 2.0.0)
biocViews
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
License
GPL-2
LazyData
true
RoxygenNote
6.0.1
NeedsCompilation
no
Packaged
2018-05-11 04:10:33 UTC; s425824
Author
Bernd Gruber [aut, cre], Arthur Georges [aut], Peter J. Unmack [ctb], Lindsay V. Clark [ctb], Oliver Berry [ctb]
Maintainer
Bernd Gruber
Repository
CRAN
Date/Publication
2018-05-11 07:25:24 UTC

install.packages('dartR')

1.0.5

4 months ago

Bernd Gruber

GPL-2

Depends on

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

Discussions