HWxtest (version 1.0.5)

observedProb: Compute observed statistics for a genotype count matrix

Description

#' Four measures of fit to Hardy-Weinberg for a given set of genotype counts may be computed.

• observedProbThe probability of the observed set under the HW null and with the allele counts fixed.
• observedLLRThe log-likelihood ratio of the observed set
• observedUThe observed U-score. Positive values indicate an excess of homozygotes and negative ones imply too many heterozygotes
• observedX2The classicalchi-squaredstatistic

Usage

observedProb(c)
observedLLR(c)
observedU(c)
observedX2(c, returnExpected = F)

Arguments

c

Matrix of observed genotype counts. Each number should be a non-negative integer, and matrix is $k x k$.

returnExpected

Used in observedX2 to indicate whether a matrix of expected numbers should be returned instead.

Value

• the observed statistic

Examples

t <- vec.to.matrix(c(0,3,1,5,18,1,3,7,5,2))
observedStats <- c(observedProb(t), observedLLR(t), observedU(t), observedX2(t))