Genetic effects {noia}R Documentation

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.

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, 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")
effectsVariances(linear)

[Package noia version 0.93 Index]