netgwas (version 0.0.1-1)

CviCol: Arabidopsis thaliana genotype data

Description

The genotype data of the Cvi-0 \(\times\) 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.

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. Behrouzi, P., and Wit, E. C. (2017c). netgwas: An R Package for Network-Based Genome-Wide Association Studies. arXiv preprint, arXiv:1710.01236. 2. Behrouzi, P., and Wit, E. C. (2017a). Detecting Epistatic Selection with Partially Observed Genotype Data Using Copula Graphical Models. arXiv preprint, arXiv:1710.00894. 3. 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)
dim(CviCol)
head(CviCol, n=3)
# }