individual_heterozygosity: Calculate individual based heterozygosity.

In hemstrow/snpR: Whole-Genome Analysis Tools for Use with Single Nucleotide Polymorphism Data

Calculate individual based heterozygosity.

Description

Calculates heterozygosity within individuals across all SNPs by either a simple ratio of heterozygous to homozygous sites or standardized for differences in genotyping success according to Coltman et al (1999).

Usage

calc_het_hom_ratio(x, facets = NULL, complex_averages = FALSE)

calc_hs(x, facets = NULL, complex_averages = FALSE)

Arguments

x	snpRdata object
facets	facets over which to split snps within samples. Takes only SNP level facets. See Facets_in_snpR for details.
complex_averages	logical, default FALSE. If TRUE, will compute weighted averages for complex (snp + sample metadata) facets. This can be quite time consuming, and so is generally not recommended unless needed.

Value

A snpRdata object with heterozygote/homozygote ratios merged into the sample.stats slot.

Functions

• calc_het_hom_ratio(): Ratio of heterozygous to homozygous sites.

• calc_hs(): H_S, Individual Heterozygosity

Het

Hom ratio:

Individual heterozygosity calculated as the number of heterozygous sites divided by the number of homozygous sites.

H_S

Calculates H_S, the mean heterozygosity of an individual standardized for unequal genotyping across individuals by dividing by the mean heterozygosity across all individuals *for the loci sequenced in that individual* (Coltman et al 1999). As a result, the global mean H_S should be roughly equal to 1, and that in 'snpR' specifically the denominator is calculated across *all individuals in all facet levels* if facets are specified instead of within populations. As a result, the weighted mean H_S in a specific population can be substantially different from one if a population is much less heterozygous.

Author(s)

William Hemstrom

References

Coltman, D. W., Pilkington, J. G., Smith, J. A., & Pemberton, J. M. (1999). Parasite-mediated selection against inbred Soay sheep in a free-living, island population. Evolution, 53(4), 1259–1267. doi: 10.1111/j.1558-5646.1999.tb04538.x

Examples

# base facet
x <- calc_het_hom_ratio(stickSNPs)
get.snpR.stats(x, stats = "het_hom_ratio")

# facet by chromosome
x <- calc_het_hom_ratio(stickSNPs, "chr")
get.snpR.stats(x, "chr", stats = "het_hom_ratio")

# Getting population means:
x <- calc_hs(stickSNPs, "pop")
get.snpR.stats(x, "pop", stats = "hs")

hemstrow/snpR documentation built on March 20, 2024, 7:03 a.m.