dartR: utils.dart2genlight – R documentation

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utils.dart2genlight

Convert DarT to genlight

Description

converts a dart file (read via read.dart) into an genlight object adegenet. Internal function called by gl.read.dart

Usage

utils.dart2genlight(
  dart,
  ind.metafile = NULL,
  covfilename = NULL,
  probar = TRUE,
  verbose = 2
)

Arguments

`dart`	a dart object created via read.dart
`ind.metafile`	optional file in csv format with metadata for each individual (see details for explanation)
`covfilename`	depreciated, use parameter ind.metafile
`probar`	show progress bar
`verbose`	– verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2]

Details

the ind.metadata file needs to have very specific headings. First an heading called id. Here the ids have to match the ids in the dart object colnames(dart[[4]]). The following column headings are optional. pop: specifies the population membership of each individual. lat and lon specify spatial coordinates (perferable in decimal degrees WGS1984 format). Additional columns with individual metadata can be imported (e.g. age, gender).

Value

a genlight object is returned. Including all available slots are filled. loc.names, ind.names, pop, lat, lon (if provided via the ind.metadata file)

dartR

Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis

v1.9.6

GPL-2

Authors

Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb]

Initial release

2021-04-29