Measure.R2 {LDcorSV}

r^2 measure

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)