Genetic effects {noia}R Documentation

Genetic Effects

Description

geneticEffects displays the geneticEffects (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, ref.genotype = "P1")
effectsVariances(obj)
effectsPvalues(reg)

Arguments

obj An object of class "noia.linear" provided by linearRegression.
ref.genotype The new reference point. Can be "F2", "F1", "Finf", "P1", "P2" (see linearRegression for details.
reg Output of a regression (object of class "lm" or "nls").

Details

The P-values can be extracted from both linear and multilinearRegressions, while the variances and the change of reference are restricted to the linear regression.

Author(s)

Arnaud Le Rouzic <a.p.s.lerouzic@bio.uio.no>

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, in press.

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")
effectsVariances(linear)

[Package noia version 0.91 Index]