CviCol: Arabidopsis thaliana genotype data

In netgwas: Network-Based Genome Wide Association Studies

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.

Author(s)

Pariya Behrouzi and Ernst C. Wit
Maintainer: Pariya Behrouzi [e-mail]

Source

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

Examples

data(CviCol)
dim(CviCol)
head(CviCol, n=3)

netgwas documentation built on Aug. 7, 2023, 5:10 p.m.