maf:
Minor alle frequencies
Description
Calculation of minor allele frequencies (MAF), call rate and asymptotic chisquare hardy-weinberg test
Usage
maf(geno, marker.label = NA)
Arguments
geno
(m, n)-genotype matrix m = number of individuals
type R: n = number of snps
marker.label
Labels for the markers.
Value
This function returns an matrix with 8 coulmns.
Details
Call rate is defined by number of missing genotypes divided by sample size.Testing deviation of the hardy-weinberg equilibirum is done by the usual
goodness-of-fit chisquare test: chi2 ~ sum( (observed-expected)^2/expected ).