enumerate_genotypes: Function for enumerating genotypes for N biallelic loci
In gpmap: Analysing and Plotting Genotype-Phenotype Maps

Description Usage Arguments Details Value Author(s) References Examples

Function for enumerating all 3^N genotypes for N biallelic loci. Optional specification of names of loci and alleles. genotypes. Generates a data frame of multilocus genotypes in the sequence used for objects of class gpmap.

1	enumerate_genotypes(nloci=1, locinames=NULL, allelenames=NULL)

`nloci`	The number of loci N
`locinames`	An optional character vector with N names of loci
`allelenames`	An optional character object specifying allele names

Unless specified locinames default to "Locus 1", "Locus 2",..,"Locus N".

If allelenames is not specified then the alleles will be named "1" and "2".

Returns a data frame with locinames as colnames, and with 3^N rows specifying all possible genotypes in the sequence used for all GP maps in the package (the same sequence as used in Gjuvsland et al.( 2011)), where the genotype at the first locus varies fastest, then the second locus, and so on:

  Locus_1 Locus_2
1      11      11
2      12      11
3      22      11
4      11      12
5      12      12
6      22      12
7      11      22
8      12      22
9      22      22

Arne B. Gjuvsland <arne.gjuvsland@nmbu.no> and Yunpeng Wang <yunpeng.wng@gmail.com>

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]

#genotypes for a single locus
enumerate_genotypes()

#genotypes for two loci "A" and "B", with alleles named "H" and "L"
enumerate_genotypes(2,c("A","B"),c("H","L"))

#genotypes for the two-locus example in Cheverud & Routman (1995)
enumerate_genotypes(2,c("D7Mit17","D1Mit7"),rbind(c('A1','A2'),c('B1','B2')))