generate_gpmap {gpmap}

Function for creating genotype-phenotype (GP) maps

Description

Function for creating a gpmap object representing a genotype-phenotype (GP) map for N biallelic loci or more generally K such maps, from a matrix of genotypic values.

Usage

 generate_gpmap(y, locinames = NULL, allelenames = NULL, mapnames = NULL) 

Arguments

y

A (3^N\times K) matrix or numeric with each column specifying the 3^N genotypic values for K GP maps

locinames

An optional character vector with N names of loci

allelenames

An optional character object specifying allele names

mapnames

An optional character vector with K names of GP maps / phenotypes

Details

Arguments locinames and allelenames are passed on to enumerate_genotypes, and the genotypic values in y should be given in the same sequence as the sequence of genotypes returned by enumerate_genotypes. If mapnames is not specified then the GP maps will be named "GPmap_1", "GPmap_2",..,"GPmap_K".

Value

The function returns an object of class gpmap containing the following components

values

The vector or matrix of genotypic values

nloci

The number of loci in the map

genotypes

Data frame with enumeration of genotypes

locinames

Character vector with names for all loci

mapname

The name(s) of the GP map

Author(s)

Arne B. Gjuvsland <[e-mail]> and Yunpeng Wang <[e-mail]>

References

Gjuvsland AB, Vik JO, Woolliams JA, Omholt SW (2011) Order-preserving principles underlying genotype-phenotype maps ensure high additive proportions of genetic variance. Journal of Evolutionary Biology 24(10):2269-2279 [link]

Examples

#inter- and intra-locus additive GPmap with two loci 
generate_gpmap(c(-2,1,0,-1,0,1,0,1,2),mapnames="Additive") 

#two-locus GP map with AxA epistasis for loci named A and B
generate_gpmap(c(-1,0,1,0,0,0,1,0,-1),locinames=c("A","B"),mapnames="AxA")

#random GP map with 3 loci
set.seed(0)
generate_gpmap(rnorm(27))