Bernd Gruber, Peter Unmack, Olly Berry and Arthur Georges

Package {dartR} is an R package for (a) loading DArT™ SNP and SilicoDArT data generated from the commercial service provided by Diversity Arrays Technology Pty Ltd; (b) applying filters to those data based on locus metadata such as call rate, information content or reproducibility; (c) assigning individuals to populations and selecting subsets of individuals or populations; (d) visualization using Principal Coordinates Analysis (PCoA); and (e) providing a conduit to a range of standard data formats and R packages for analysis.

In most cases, the scripts in {dartR} are simple wrappers for scripts included in other already available packages, to provide transparent access to these packages for analyzing DArT data, and to provide some enhanced output diagnostics. Relatively few scripts provide novel analyses. We make no apologies for this, as the objective of {dartR} is to provide fundamental tools for accessing and manipulating DArT datafiles in preparation for analysis by the vast suite of packages available in R through the CRAN repository.

A summary of the capabilities of {dartR} is as follows:

• Intelligent interpretation and input of DArT Pty Ltd comma-delimited files to a compact genlight form of the R {adegenet} package.
• Filtering loci and individuals on criteria drawn from the DArT locus metadata (such as repAvg, AvgPIC) or on computed statistics (such as call rate).
• Relabelling individuals and recoding populations into new aggregations, and deleting selected individuals or populations.
• Visualization using Principal Coordinates Analysis (PCoA) and other visual tools.
• Conversion of data to other R packages (e.g. NewHybrids), to other {adegenet} objects (e.g. genind), and to standard data formats (e.g. fastA).
• A few specific analyses not available elsewhere (e.g. fixed difference analysis, assignment analysis).

Installing dartR

CRAN version

install.packages("dartR")
library(dartR)

Latest stable version

install.packages("devtools")
library(devtools) install_github("green-striped-gecko/dartR")
ibrary(dartR)

Beta version

install.packages("devtools")
library(devtools) install_github("green-striped-gecko/dartR", ref="dev")
library(dartR)

The package dartR has recently been announced in Molecular Ecology Resources.

A Q&A forum called dartR has been established on Google Groups to assist with issues as they arise. You are welcome to join.