utils.dart2genlight: An internal function to converts DarT to genlight.

In dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions

An internal function to converts DarT to genlight.

Description

WARNING: UTILITY SCRIPTS ARE FOR INTERNAL USE ONLY AND SHOULD NOT BE USED BY END USERS AS THEIR USE OUT OF CONTEXT COULD LEAD TO UNPREDICTABLE OUTCOMES.

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

Converts a DArT file (read via read.dart) into an genlight object from package adegenet. #' Internal function called by gl.read.dart().

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)

Author(s)

Maintainer: Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)

See Also

Other utilities: gl.alf(), utils.check.datatype(), utils.collapse.matrix(), utils.dist.binary(), utils.flag.start(), utils.hamming(), utils.het.pop(), utils.impute, utils.is.fixed(), utils.jackknife(), utils.n.var.invariant(), utils.plot.save(), utils.read.fasta(), utils.read.ped(), utils.recalc.avgpic(), utils.recalc.callrate(), utils.recalc.freqhets(), utils.recalc.freqhomref(), utils.recalc.freqhomsnp(), utils.recalc.maf(), utils.reset.flags(), utils.transpose(), utils.vcfr2genlight.polyploid()

dartR.base documentation built on April 4, 2025, 2:45 a.m.