exampleRAD

exampleRAD_mapping

Msi01genes

<p><code>exampleRAD</code> and <code>exampleRAD_mapping</code> are two very small
simulated <code>"RADdata"</code> datasets for testing polyRAD
functions.  Each has four loci.  <code>exampleRAD</code> is a 
natural population of 100 individuals with a mix of diploid and tetraploid 
loci, with 80 individuals diploid and 20 individuals triploid.
<code>exampleRAD_mapping</code> is a diploid BC1 mapping population with two parents
and 100 progeny.
<code>Msi01genes</code> is a <code>"RADdata"</code> object with 585 taxa and 24 loci,
containing real data from <em>Miscanthus sinensis</em>, obtained by using
<code>VCF2RADdata</code> on the file Msi01genes.vcf.  Most individuals
in <code>Msi01genes</code> are diploid, with three haploids and one triploid.</p>

datasets

Read depth data from genotyping-by-sequencing (GBS) or restriction
site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian
probability estimates of genotypes in polyploids or diploids.  The genotype
probabilities, posterior mean genotypes, or most probable genotypes can then
be exported for downstream analysis.  'polyRAD' is described by Clark et al.
(2019) <doi:10.1534/g3.118.200913>, and the Hind/He statistic for marker
filtering is described by Clark et al. (2022) <doi:10.1186/s12859-022-04635-9>.
A variant calling pipeline for highly duplicated genomes is also included and
is described by Clark et al. (2020, Version 1) <doi:10.1101/2020.01.11.902890>.

exampleRAD: Miniature Datasets for Testing polyRAD Functions

Description

Usage

Arguments

Format

Examples