HardyWeinberg: HWData – R documentation

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HWData

Generate genetic marker data in or out of Hardy-Weinberg Equilibrium

Description

HWData generates samples of genotypic counts under various schemes. It mainly uses sampling from the multinomial distribution given Hardy-Weinberg allele frequencies.

Usage

HWData(nm = 100, n = rep(100, nm), f = rep(0, nm), p = NULL, conditional
= FALSE, exactequilibrium = FALSE, pdist = "runif", x.linked = FALSE, nA
= NULL,
n.males=rep(round(0.5*n),nm), ...)

Arguments

`nm`	The number of bi-allelic markers.
`n`	The sample sizes.
`f`	The inbreeding coefficients (only for autosomal markers)
`p`	a vector of allele frequencies
`conditional`	if `TRUE` Haldane's distribution is used for sampling, if `FALSE` a multinomial distribution is used. Replaces parameter `pfixed` from the previous version of the package
`exactequilibrium`	generates data in exact HWE if set to `TRUE`
`pdist`	Take a random allele frequency from a uniform or beta distribution of `pfixed = FALSE` and `p` is not given.
`x.linked`	Simulated autosomal markers (`x.linked=FALSE`, the default) or X-chromosomal markers (`x.linked=TRUE`)
`nA`	A vector of minor allele counts, one for each marker. If not specified, it will be calculated from `p`
`n.males`	The number of males (only relevant if `x.linked = TRUE`)
`...`	specific parameters for the uniform or beta

Details

The exactequilibrium option only takes effects for autosomal markers (x.linked=FALSE) and multinomial sampling (conditional=FALSE).

Option pfixed is deprecated and replaced by conditional

HWData returns a matrix of genotype counts, nm by 3 for autsomal markers or nm by 5 for X-chromosomal markers. Output is no longer supplied in the compositional form. Function HWClo can be used to convert the genotype counts to a composition.

If the inbreeding coefficient is specified (f) it will only take effect for autosomal markers (x.linked=FALSE) and multinomial sampling (conditional=FALSE).

Value

`X`	A matrix containing the genotype counts.

Author(s)

Jan Graffelman (jan.graffelman@upc.edu)

Examples

nm <- 100
n <- 100
out <- HWData(nm,n)

HardyWeinberg

Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

v1.7.2

GPL (>= 2)

Authors

Jan Graffelman [aut, cre], Christopher Chang [ctb], Xavi Puig [ctb], Jan Wigginton [ctb], Leonardo Ortoleva [ctb], William R. Engels [ctb]

Initial release

2021-04-28