testgenotypes

<code>genambig</code> object containing alleles of 20 Rubus
 samples at three microsatellite loci.

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

Alistair J. Hall

Handunnethi Nihal de Silva

Tyler William Smith

testgenotypes function

A <code>genambig</code> object with data in the <code>Genotypes</code>,
 <code>PopInfo</code>, <code>PopNames</code>, and <code>Usatnts</code> slots. This is
 saved as a .RData file. Population identities are used here to
 indicate two different species.

Format

Rubus Genotype Data for Learning polysat — testgenotypes

Rubus Genotype Data for Learning polysat

testgenotypes: Rubus Genotype Data for Learning polysat

Description

Usage

Arguments

Format

See Also