dstat: Tomoka Ohta's D Statistics

In ohtadstats: Tomoka Ohta D Statistics

Description

Implements Ohta's D statistics for a pair of loci. Statistics are returned in a vector in the following order: Number of populations, D2it, D2is, D2st, D'2st, D'2is.

Usage

dstat(index, data_set, tot_maf = 0.1, pop_maf = 0.05)

Arguments

index	A two-element vector of column names or numbers for which Ohta's D Statistics will be computed.
data_set	Matrix containing genotype data with individuals as rows and loci as columns. Genotypes should be coded as 0 (homozygous), 1 (heterozygous), or 2 (homozygous). Rownames must be subpopulation names and column names should be marker names.
tot_maf	Minimum minor allele frequency across the total population for a marker to be included in the analysis.
pop_maf	Minimum minor allele frequency across a subpopulation for that subpopulation to be included in analysis.

Details

When the loci being evaluated fail to pass the filtering thresholds determined by tot_maf and pop_maf, NAs are returned.

Value

nPops Number of subpopulations used for computation, after filtering.

D2it A measure of the correlation of alleles at two loci on the same gametes in a subpopulation relative to their expectation according to allele frequencies in the total population.

D2is Expected variance of LD for subpopulations.

D2st Expected correlation of alleles in a subpopulation relative to their expected correlation in the total population.

Dp2st Variance of LD for the total population computed over alleles only.

Dp2is Correlation of alleles at two loci on the same gamete in subpopulations relative to their expected correlation in the total population.

References

Beissinger et al. (2016) Heredity. (https://www.nature.com/articles/hdy201581) & Ohta. (1982) Proc. Natl. Acad. Science. (http://www.pnas.org/content/79/6/1940)

Examples

data(beissinger_data)
dstat(index = c(5,6), data_set = beissinger_data)

ohtadstats documentation built on Nov. 15, 2019, 5:11 p.m.