HWData: Generate genetic marker data in or out of Hardy-Weinberg...

In HardyWeinberg: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

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 for given or random allele frequencies, either assuming Hardy-Weinberg proportions or a specified degree of inbreeding. Sampling can also be performed conditional on the allele frequency. The same procedures are also available for X linked markers.

Usage

HWData(nm = 100, n = rep(100, nm), f = rep(0, nm), p = NULL, conditional = FALSE,
exactequilibrium = FALSE, x.linked = FALSE, nA = NULL, n.males = round(0.5 * n),
shape1 = 1, shape2 = 1, counts = TRUE)

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 The Levene-Haldane distribution will be used for sampling autosomal markers, the Graffelman-Weir distribution for sampling X chromosomal markers. If FALSE a multinomial distribution is used
exactequilibrium	generates data in exact HWE if set to TRUE
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)
shape1	First shape parameter of the beta distribution used to generate allele frequencies
shape2	Second shape parameter of the beta distribution used to generate allele frequencies
counts	If counts=TRUE the output are genotype counts, if counts=TRUE relative genotype frequencies

Details

Option pfixed is deprecated and replaced by conditional Option pdist is deprecated and replaced by parameters shape1 and shape2

HWData returns a matrix of genotype counts, nm by 3 for autsomal markers or nm by 5 for X-chromosomal markers.

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 ([e-mail])

See Also

HWTernaryPlot

Examples

#
# Generate 100 SNPs with uniform allele frequency under the equilibrium assumption.
#
out <- HWData(nm=100,n=100)
#
# Generate genotype frequencies of 100 SNPs with uniform allele frequency assuming exact equilbrium.
#
X <- HWData(nm=100, exactequilibrium = TRUE, counts = FALSE)
#
# Generate 100 SNPs (as counts), all having an expected A allele frequency of 0.50
#
X <- HWData(nm=100,p=0.5)
#
#  Generate 100 SNPs, 50 with A allele frequency 0.25 and 50 with A allele frequency 0.75,
#  assuming fixed allele frequencies. 
#
X <- HWData(nm=100,p=rep(c(0.25,0.75),50), conditional = TRUE)
#
#  Generate 100 SNPs with a skewed (beta) distribution of the allele frequency,
#  rich in variants with a low minor allele frequency.
#
X <- HWData(nm=100,shape1=1,shape2=10)
#
# Generate 100 X chromosomal SNPs with uniformly distributed allele frequency.
#
X <- HWData(nm=100, x.linked = TRUE)

HardyWeinberg documentation built on May 29, 2024, 6:17 a.m.