epistasis (version 0.0.1-1)

CviCol: Arabidopsis thaliana genotype data

Description

The genotype data of the Cvi-0 x Col-0 Recombinant Inbred Line (RIL) population.

Usage

data(CviCol)

Format

The format is a matrix containing 90 single-nucleotide polymorphism (SNP) markers for 367 individuals.

Source

It is publicly available at http://publiclines.versailles.inra.fr/page/8

Details

The Arabidopsis thaliana genotype data is derived from a RIL cross between Columbia-0 (Col-0) and the Cape Verde Island (Cvi-0), where 367 individuals were genotyped for 90 genetic markers. This is a diploid population with three possible genotpe states (k = 3), where the genotypes coded as 0, 1, 2, where 0 and 2 represent the homozygous genotypes and 1 defines the heterozygous genotype. This data set can be used to detect epistatic selection, short- and long- range linkage disequilibrium between 90 SNP markers.

References

1. P. Behrouzi and E. C. Wit. Detecting Epistatic Selection with Partially Observed Genotype Data Using Copula Graphical Models. arXiv, 2016. 2. Simon, M., et al. "QTL mapping in five new large RIL populations of Arabidopsis thaliana genotyped with consensus SNP markers." Genetics 178 (2008): 2253-2264.

Examples

## Not run: 
# data(CviCol)
# 
# # Graph path
# epi <- epistasis(CviCol, method="approx", rho.ratio=0.2)
# epi
# plot(epi)
# 
# sel <- episelect(epi)
# plot(sel)
# ## End(Not run)