NOIA package {noia}R Documentation

Implementation of the Natural and Orthogonal InterAction (NOIA) model

Description

The NOIA model, as described extensively in Alvarez-Castro & Carlborg (2007) Genetics 176: 1151-1167, is a framework facilitating the estimation of geneticEffects and genotype-to-phenotype maps. This package provides the basic tools to perform linear and multilinearRegressions from real populations (provided the phenotype and the genotype of every individuals), estimating the geneticEffects from different reference points, the genotypic values, and the decomposition of genetic variances in a multi-locus, 2 alleles system

Details

Package: noia
Type: Package
Version: 0.91
Date: 2008-04-25
License: GPL v 2

Data set
The user must provide (i) a vector of the phenotypes measured in the population, and (ii) a matrix of the genotypes. There are two input formats for the genotype, see linearRegression
Regression functions
linearRegression and multilinearRegression
Change of reference
geneticEffects
Genotype-to-phenotype map
GPmap
Decomposition of genetic variance
varianceDecomposition

Author(s)

Arnaud Le Rouzic

Maintainer: 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.

Alvarez-Castro JM, Le Rouzic A, Carlborg O. (2008). How to perform meaningful estimates of genetic effects. PLoS Genetics, in press.

Le Rouzic A, Alvarez-Castro JM. (2008). Estimation of genetic effects and genotype-phenotype maps. Evolutionary Bioinformatics, in press.

Examples

set.seed(123456789)

map <- c(0.25, -0.75, -0.75, -0.75, 2.25, 2.25, -0.75, 2.25, 2.25)
names(map) <- genNames(2)
pop <- simulatePop(map, N=500, sigmaE=0.2, type="F2")

# Regressions

linear <- linearRegression(phen=pop$phen, gen=pop[2:3])

multilinear <- multilinearRegression(phen=pop$phen, gen=cbind(pop$Loc1, 
        pop$Loc2))

# Linear effects, associated variances and stderr
linear

# Multilinear effects
multilinear

# Change of reference: geneticEffects in the "11" genotype (parental 1)
geneticEffects(linear, ref.genotype="P1")

# Variance decomposition
varianceDecomposition(linear)

# GP maps
maps <- cbind(map, GPmap(linear)[,1], GPmap(multilinear)[,1])
colnames(maps) <- c("Actual", "Linear", "Multilinear")
maps

[Package noia version 0.91 Index]