simgen

<p><code>genambig</code> object containing simulated data from three
  populations with 100 individuals each, at three loci.  Individuals
  are a random mixture of diploids and tetraploids.  Genotypes were
  generated according to pre-set allele frequencies.</p>

datasets

A collection of tools to handle microsatellite data of
any ploidy (and samples of mixed ploidy) where allele copy number is not
known in partially heterozygous genotypes.  It can import and export data in
ABI 'GeneMapper', 'Structure', 'ATetra', 'Tetrasat'/'Tetra', 'GenoDive', 'SPAGeDi',
'POPDIST', 'STRand', and binary presence/absence formats.  It can calculate
pairwise distances between individuals using a stepwise mutation model or
infinite alleles model, with or without taking ploidies and allele frequencies
into account.  These distances can be used for the calculation of clonal
diversity statistics or used for further analysis in R.  Allelic diversity
statistics and Polymorphic Information Content are also available.  polysat can
assist the user in estimating the ploidy of samples, and it can estimate allele
frequencies in populations, calculate pairwise or global differentiation statistics
based on those frequencies, and export allele frequencies to 'SPAGeDi' and 'adegenet'.
Functions are also included for assigning alleles to isoloci in cases where one pair
of microsatellite primers amplifies alleles from two or more independently
segregating isoloci.  polysat is described by Clark and Jasieniuk (2011)
<doi:10.1111/j.1755-0998.2011.02985.x> and Clark and Schreier (2017)
<doi:10.1111/1755-0998.12639>.

Lindsay V Clark

polysat

Tools for Polyploid Microsatellite Analysis

Lindsay V. Clark

Alistair J. Hall

Handunnethi Nihal de Silva

Tyler William Smith

simgen function

<p>A <code>genambig</code> object with data in the <code>Genotypes</code>,
  <code>PopInfo</code>, <code>PopNames</code>, <code>Ploidies</code> and <code>Usatnts</code>
  slots.  This is saved as an .RData file.  <code>simgen</code> was created
  using the code found in the &#8220;simgen.R&#8221; file in the
  &#8220;extdata&#8221; directory of the polysat package installation.  This
  code may be useful for inspiration on how to create a simulated dataset.</p>

Format

Randomly Generated Data for Learning polysat — simgen

Randomly Generated Data for Learning polysat

simgen: Randomly Generated Data for Learning polysat

Description

Usage

Arguments

Format

See Also