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.
utils.dart2genlight(
dart,
ind.metafile = NULL,
covfilename = NULL,
probar = TRUE,
verbose = NULL
)A genlight object. Including all available slots are filled. loc.names, ind.names, pop, lat, lon (if provided via the ind.metadata file)
A dart object created via read.dart [required].
Optional file in csv format with metadata for each individual (see details for explanation) [default NULL].
Depreciated, use parameter ind.metafile.
Show progress bar [default TRUE].
Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default NULL].
Maintainer: Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)
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).
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()