calc.gene.var: Genetic Variance

In SimPhe: Tools to Simulate Phenotype(s) with Epistatic Interaction

Description

Calculate the total genetic variance

Usage

calc.gene.var(gene.coef, freq, Dskim = 0, ...)

Arguments

gene.coef	a list with the coefficients of genetic effects. Each element includes 8 genetic parameters (regression coefficient) β_Gwt, t in (1, 2, ..., 8)
freq	a dataframe with the allele frequencies.
Dskim	the coefficient of linkage disequilibrium. Default is 0 (no LD).
...	not used.

Details

The genetic variance is calculated based on the genetic parameters β_Gwt, t in (1, 2, ..., 8).

as described in the publications by Kao and Cockerham:

Kao CH, Zeng ZB. Modeling epistasis of quantitative trait loci using Cockerham's model. Genetics. 2002 Mar 1;160(3):1243-61.
http://www.genetics.org/content/160/3/1243.short

Cockerham CC, Weir BS. Quadratic analyses of reciprocal crosses. Biometrics. 1977 Mar 1:187-203.
http://www.jstor.org/stable/2529312

Value

genetic variance.

Author(s)

Beibei Jiang [e-mail]

Examples

calc.gene.var(gene.coefficients, allele.freq)

SimPhe documentation built on May 1, 2019, 9:10 p.m.