effectsNames: Names of Genetic Effects

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

Names of Genetic Effects

Description

Provides and manipulates labels of genetic effects.

Usage

effectsNamesGeneral(nloc = 2, max.level=NULL, max.dom=NULL) 
effectsNamesMultilinear(nloc=2, max.level=2, max.dom=2)

Arguments

nloc	Number of loci.
max.level	Maximum order of interactions.
max.dom	Maximum order for dominance.

Details

The codes for genetic effects are stored into a vector of length 4, effectsNames. The first element of the vector is the code for the absence of effect (default: "."). The three other elements are respectively additive effects (default: "a") dominance effects (default: "d"), and multilinear epistatic effects (default: "e").

The names of genetic effects contains as many characters as the number of loci in the system. The additive effect of the first locus in a 3-locus system will be "a..", and the "Dominance by Dominance" between loci 2 and 4 in a 5-locus system will be ".d.d.". Directionality of epistasis between two (or more) loci is indicated by as many "e" as necessary (e.g. ".ee." for the interaction between loci 2 and 3 in a 4-locus case).

effectsNamesGeneral and effectsNamesMultilinear provide a list of the names of the genetic effects, in the correct order to be processed in the NOIA framework (Alvarez-Castro and Carlborg 2007).

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

geneticEffects, genNames, linearRegression, multilinearRegression.

Examples

effectsNamesGeneral(3)
  

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