genetic.scale: Genetic scales of epistatic model

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

Description

Genetic scales of epistatic model (Cockerham model) based on F2 population.

Usage

genetic.scale(SNPA = 0, SNPB = 0)

Arguments

SNPA	encoded alleles for first SNP.
SNPB	encoded alleles for second SNP.

Details

Calculate the genetic scale for a given allele combination of two SNPs. There are 9 genotypes in an F2 population, so we need 8 genetic parameters to give a complete description of the values for the 9 genotypes. Under the assumption of Hardy-Weinberg and linkage equilibrium, Cockerham (1954)'s orthogonal partition of genetic variance leads to the definition of the genotypic value G_{ij}

G_{ij}=β_{0}+∑_{t=1}^{8}β_{G_{w_{t}}}w_{tij}

by eight orthogonal scales or contrasts w_{t}'s, t in (1, 2, ..., 8). Four are marginal scales and four are interaction scales. Marginal scales (defined by Model I for an F2 population) are called linear and quadratic scales (additive and dominance scales in genetic terms). Correspondingly, the interaction scales are

w1

additive for locus A;

w2

dominance for locus A;

w3

additive for locus B;

w4

dominance for locus B;

w5 (= w1 * w3)

linear * linear, additive * additive;

w6 (= w1 * w4)

linear * quadratic, additive * dominance;

w7 (= w2 * w3)

quadratic * linear, dominance * additive;

w8 (= w2 * w4)

quadratic * quadratic, dominance * dominance.

SNPs are encoded by (0, 1, 2):

0

means homozygous with major alleles;

1

means heterozygote;

2

means homozygous with minor alleles

E.g., the SNPs are encoded as 0: AA, 1: AG, and 2: GG, where 'A' represents the major allele and 'G' the minor allele.

Value

a vector of genetic scales.

Author(s)

Benno Pütz [e-mail] and Beibei Jiang [e-mail]

Examples

genetic.scale(SNPA = 1, SNPB = 0)

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