mixIndependR (version 0.3.0)

HWE.Fisher: Test the Hardy Weinberg Equilibrium with Fisher's exact test###

Description

Test the Hardy Weinberg Equilibrium with Fisher's exact test###

Usage

HWE.Fisher(p,H,y)

Arguments

p

a matrix of allele frequency;each row denotes allele; each column denotes each loci;

H

a vector of number of Heterozygotes on each loci; length is number of loci.

y

a matrix of observed genotype Densities(Not count). Each row denotes each genotype; each column denotes each loci. The order of markers follows x; the genotypes are ordered by: from 1:l-th column, the genotypes are homozygous in order as : p1p1, p2p2,p3p3,...,plpl;from ll-th to u-th column, the genotypes are heterozygous in order as:choose(l,2) like: p1p2,p1p3,...,p1pl,p2p3,p2p4,...p2pl,...p(l-1)pl

Value

a vector of p-values of Fisher's test; ordered by the order of loci in p or x

Details

This function check the Hardy Weinberg Equilibrium with Fisher's exact Test.#####

References

Weir, B. S. (1996, ISBN:9780878939022)

Examples

# NOT RUN {
x <- data.frame(STR1=c(12,13,13,14,15,13,14,12,14,15),
               STR1_1=c(12,14,13,15,13,14,13,12,14,15),
               SNP1=c("A","T","A","A","T","A","A","T","T","A"),
               SNP1_1=c("A","T","T","T","A","T","A","A","T","T"))
p <-AlleleFreq(x)
G <- GenotypeFreq(x,p,expect = FALSE)
h <- Heterozygous(x)
H <- RxpHetero(h,p,HWE = FALSE)
HWE.Fisher(p,H,G/colSums(G))

# }