utils.dart2genlight: Converts DarT to genlight

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Converts 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 = NULL
)

Arguments

dart	A dart object created via read.dart [required].
ind.metafile	Optional file in csv format with metadata for each individual (see details for explanation) [default NULL].
covfilename	Depreciated, use parameter ind.metafile.
probar	Show progress bar [default TRUE].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default NULL].

Details

The ind.metadata file needs to have very specific headings. First a 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 (in decimal degrees WGS1984 format). Additional columns with individual metadata can be imported (e.g. age, gender).

Value

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

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.