exampleRAD

exampleRAD_mapping

Msi01genes

<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.
<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 Miscanthus sinensis, obtained by using
<code>VCF2RADdata</code> on the file Msi01genes.vcf.

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>. A variant calling pipeline for highly
duplicated genomes is also included and is described by Clark et al. (2020)
<doi:10.1101/2020.01.11.902890>.

Lindsay V Clark

polyRAD

Genotype Calling with Uncertainty from Sequencing Data in
Polyploids and Diploids

Lindsay V. Clark

U.S. National Science Foundation 

exampleRAD function

See the format described in <code>"RADdata"</code>.

Format

Miniature Datasets for Testing polyRAD Functions — exampleRAD

Miniature Datasets for Testing polyRAD Functions

exampleRAD: Miniature Datasets for Testing polyRAD Functions

Description

Usage

Arguments

Format

Examples