hwe {gap} | R Documentation |
Hardy-Weinberg equilibrium test
hwe(data,yates.correct=FALSE, miss.val=0) hwe(data,is.genotype=FALSE, yates.correct=FALSE, miss.val=0) hwe(data,is.count=FALSE, yates.correct=FALSE, miss.val=0)
data |
a rectangular data containing the genotype, or an array of genotype counts |
is.genotype |
A flag indicating if the data is an array of genotypes |
is.count |
A flag indicating if the data is an array of genotypes count |
yates.correct |
A flag indicating if Yates' correction is used for Pearson chi-squared statistic |
miss.val |
A list of missing values |
This function obtains Hardy-Weinberg equilibrium test statistics. It can handle data coded as allele numbers (default), genotype identifiers (by setting is.genotype=TRUE) and counts corresponding to individual genotypes (by setting is.count=TRUE) ; the latter does not need is.genotype to be specified but requires that genotype counts for all possible genotypes, i.e. n(n+1)/2, where n is the number of alleles.
The returned value is a list containing:
x2 |
Pearson chi-square |
p.x2 |
p value for chi-square |
lrt |
Log-likelihood ratio test statistic |
p.lrt |
p value for lrt |
df |
Degree(s) of freedom |
rho |
chi-square/N the effect size |
Jing hua Zhao
## Not run: a <- c(3,2,2) a.out <- hwe(a,is.genotype=TRUE) a.out a.out <- hwe(a,is.count=TRUE) a.out ## End(Not run)