exampleRAD: Miniature Datasets for Testing polyRAD Functions

In polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

Miniature Datasets for Testing polyRAD Functions

Description

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

Usage

data(exampleRAD)
data(exampleRAD_mapping)
data(Msi01genes)

Format

See the format described in "RADdata".

Source

Randomly generated using a script available in polyRAD/extdata/simulate_rad_data.R.

M. sinensis sequencing data available at https://www.ncbi.nlm.nih.gov//bioproject/PRJNA207721, with full genotype calls at doi: 10.13012/B2IDB-1402948_V1.

Examples

data(exampleRAD)
exampleRAD
data(exampleRAD_mapping)
exampleRAD_mapping
data(Msi01genes)
Msi01genes

polyRAD documentation built on Nov. 10, 2022, 5:14 p.m.