Measure.R2: r^2 measure

In LDcorSV: Linkage Disequilibrium Corrected by the Structure and the Relatedness

Description

This function estimates the usual measure of linkage disequilibrium (r^2) between two loci.

Usage

Measure.R2(biloci, na.presence = TRUE)

Arguments

biloci	Numeric matrix (N x 2), where N is the number of genotypes (or haplotypes) Matrix values are the allelic doses: - (0,1,2) for genotypes. - (0,1) for haplotypes. Rows names correspond to the ID of individuals. Columns names correspond to the ID of markers.
na.presence	Boolean indicating the presence of missing values in data. If na.presence=FALSE (no missing data), computation of r^2_V and r^2_{VS} is largely optimized. By default, na.presence=TRUE.

Value

The returned value is the estimated value of the usual measure of linkage disequilibrium (r^2) or NA if less than 5 individuals have non-missing data at both loci

Author(s)

David Desrousseaux, Florian Sandron, Aurélie Siberchicot, Christine Cierco-Ayrolles and Brigitte Mangin

References

Hill, W.G, Robertson, A. (1968). Linkage diseqilibrium in finite populations. Theoretical and Applied Genetics, 38, 226-231. DOI: 10.1007/BF01245622

Examples

data(data.test)
Geno <- data.test[[1]]
Measure.R2(Geno)

Example output

[1] 0.0954443

LDcorSV documentation built on Aug. 26, 2020, 9:06 a.m.