estimate_rel: Estimate relatedness values

In andersgs/irelr: Pedigree Inference using Molecular Marker Data

Description

Estimate relatedness values

Usage

estimate_rel(data, input_allele_f = NULL)

Arguments

data	A GENIND class object
input_allele_f	A vector of allele frequencies (optional)

Details

Queller and Goodnight (1989)

r_{QG89_{xy}} = sum_{l}((sum(p_xm - p_m)) / sum_{l}(sum(p_ym - p_m)))

r_{QG89_{yx}} = sum_{l}((sum(p_ym - p_m)) / sum_{l}(sum(p_xm - p_m)))

Value

A data.frame with (n * (n - 1)) \ 2 (where n is the number of genotypes) rows of pairwise relatedness values for a number of relatedness indices.

• ind1, ind2: Pair of individuals for which relatedness values refer to.

• n_missing_loci: number of missing loci in the two individuals.

• QG89_xy: Queller and Goodnight (1989) index with ind1 as the numerator and ind2 as the denominator.

• QG89_yx: Queller and Goodnight (1989) index with ind2 as the numerator and ind1 as the denominator.

• QG89_avg: the mean of QG89_xy and QG89_yx.

• QG89_rsxy: sum of the numerators of QG89_xy and QG89_yx divided by the sum of the denominators of QG89_xy and QG89_yx.

• LR99_avg: the mean of the Lynch and Ritland (1999) index calculated with ind1 as the reference individual, and ind2 as the reference.

• W02_unc: the uncorrected Wang (2002) index.

• W02_cor: the corrected Wang (2002) index.

• prop_allele_shared: proportion of alleles that are shared between ind1 and ind2.

• prop_loci_shared: proportion of loci that are that have at least one allele in common between ind1 and ind2.

• missing_loci: id of missing loci.

References

Queller and Goodnight. 1989.

Lynch and Ritland. 1999.

Examples

library(adegenet)
data(nancycats)
estimate_rel(data = nancycats)

andersgs/irelr documentation built on May 12, 2019, 2:41 a.m.