Genetic effects: Genetic Effects

Description

geneticEffects displays the genetic effects (and their standard errors) from the result of linearRegression. If a new reference point is provided, a "change of reference" operation is performed (Alvarez-Castro and Carlborg 2007). effectsPvalues and effectsVariances display respectively the P-value (probability for the effect to be = 0) and the part of genetic variance due to this effect.

Usage

geneticEffects(obj, reference="P1", ref.genotype = NULL)
effectsVariances(obj)
effectsPvalues(reg)

Arguments

obj

An object of class "noia.linear" provided by linearRegression.

reference

The new reference point. Can be "F2", "F1", "Finf", "P1", "P2" (see linearRegression for details.

ref.genotype

The same as reference, provided for compatibility with older versions.

reg

Output of a regression (object of class "lm" or "nls").

Details

The P-values can be extracted from both linear and multilinear regressions. However, variance decomposition and change of reference operation are not possible from the result of a multilinear regression.

References

Alvarez-Castro JM, Carlborg O. (2007). A unified model for functional and statistical epistasis and its application in quantitative trait loci analysis. Genetics 176(2):1151-1167.

Le Rouzic A, Alvarez-Castro JM. (2008). Estimation of genetic effects and genotype-phenotype maps. Evolutionary Bioinformatics, 4.

Examples

Run this code

map <- c(0.25, -0.75, -0.75, -0.75, 2.25, 2.25, -0.75, 2.25, 2.25)
pop <- simulatePop(map, N=500, sigmaE=0.2, type="F2")

# Regressions

linear <- linearRegression(phen=pop$phen, gen=cbind(pop$Loc1, pop$Loc2))

geneticEffects(linear, "P1")
effectsVariances(linear)