paramlink: allGenotypes – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

allGenotypes

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.

Author(s)

Magnus Dehli Vigeland

Examples

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

paramlink

Parametric Linkage and Other Pedigree Analysis in R

v1.1-2

GPL (>= 2)

Authors

Magnus Dehli Vigeland [aut, cre], Thore Egeland [ctb], Guro Doerum [ctb]

Initial release

2018-01-05