geneticEffects: Genetic Effects

In noia: Implementation of the Natural and Orthogonal InterAction (NOIA) Model

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).

Usage

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

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.

Details

Variance decomposition and change of reference operation are not possible from the result of a multilinear regression.

Author(s)

Arnaud Le Rouzic

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.

See Also

linearRegression, multilinearRegression.

Examples

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")

noia documentation built on March 31, 2023, 6:45 p.m.