Effects names {noia}R Documentation

Names of Genetic Effects

Description

Provides and manipulates labels of geneticEffects.

Usage

effectsNamesGeneral(nloc = 2)   
effectsNamesMultilinear(nloc=2, max.level=2, max.dom=2)
effectsSelect(nloc, max.level=NULL, max.dom=NULL)
effNames(effects=NULL, loci=NULL, nloc=1)

Arguments

nloc Number of loci.
max.level Maximum level of interactions.
max.dom Maximum level of dominance.
effects Vector of characters.
loci Vector of locus positions.

Details

The codes for geneticEffects 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 geneticEffects 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 geneticEffects, in the right orders to be processed by the NOIA framework (Alvarez-Castro and Carlborg 2007).

effNames is a low-level routine, called by the other functions. It provides names "on demand", for instance effNames(c("a","d"),c(2,4),5) will generate ".a.d.", i.e. an "a" at locus 2 and a "d" at locus 4, in a set of 5 loci.

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

geneticEffects, genNames, linearRegression, multilinearRegression.

Examples

effectsNamesGeneral(3)
effectsSelect(nloc=3, max.level=1)
  

[Package noia version 0.91 Index]