allGenotypes {paramlink}

Genotype combinations

Description

Auxiliary functions computing possible genotype combinations in a pedigree. These are not normally intended for end users.

Usage

allGenotypes(n)

fast.grid(argslist, as.list = FALSE)

geno.grid.subset(x, partialmarker, ids, chrom, make.grid = T)

Arguments

n

a positive integer.

argslist

a list of vectors.

as.list

if TRUE, the output is a list, otherwise a matrix.

x

a linkdat object.

partialmarker

a marker object compatible with x.

ids

a numeric with ID labels of one or more pedigree members.

chrom

a character, either 'X' or 'AUTOSOMAL'. If missing, the 'chrom' attribute of partialmarker is used. If this is also missing, then 'AUTOSOMAL' is taken as the default value.

make.grid

a logical. If FALSE, a list is returned, otherwise fast.grid is applied to the list before returning it.

Value

allGenotypes returns a matrix with 2 columns and n + n*n(n-1)/2 rows containing all possible (unordered) genotypes at a biallelic locus with alleles 1,2,...{},n. fast.grid is basically a stripped down version of expand.grid.

Examples

m = allGenotypes(2)
stopifnot(m == rbind(c(1,1), c(2,2), 1:2))