normalised_LD: Computation of normalised linkage disequillibrium.

In xthchen/haplotest: Haplotype based testing for evolve and resequence

Computation of normalised linkage disequillibrium.

Description

Compute Linkage Disequillibrium(LD) between 2 SNPs, return normalised LD (Lewontin, R. C. 1964) and estimated variance of normalised LD (Zapata, C. et al. 1997).

Usage

normalised_LD(SNP_1, SNP_2, haplotype, frequency_matrix, allele_frequency)

Arguments

SNP_1	Numeric, SNP position of SNP 1
SNP_2	Numeric, SNP position of SNP 2
haplotype	Binary numeric matrix containing information of haplotype structure. The columns corresponds to the haplotypes and the rows to the SNPs.
frequency_matrix	Numeric matrix, with each i,j element being the frequency of haplotype i at sequenced time point j.
allele_frequency	Numeric matrix, with each i,j element being the frequency of SNP i at sequenced time point j.

Value

A numeric vector with its first element being the normalised LD, second element the estimated variance of normalised LD.

References

Lewontin, R. C., (1964), The Interaction of Selection and Linkage. I. General Considerations; Heterotic Models, Genetics 49(1): 49–67.

Zapata, C., Alvarez, G., Carollo, C., (1997), Approximate variance of the standardized measure of gametic disequilibrium D’, American journal of human genetics 61(3): 771–774.

See Also

haplotest()

xthchen/haplotest documentation built on Nov. 29, 2022, 12:07 p.m.