Allele frequencies and marker summaries

Computes, for every marker, the frequency of the counted allele, the minor allele frequency, the call rate and the observed heterozygosity.

Usage

alleleFrequency(x, ...)

# S4 method for class 'BreedingExperiment'
alleleFrequency(x, ...)

Arguments

x

A BreedingExperiment object.

...

Unused.

Value

A S4Vectors::DataFrame with one row per marker and columns freq, maf, callRate and heterozygosity.

Examples

set.seed(1)
be <- simulateBreeding(n_ind = 30, n_marker = 50)
head(alleleFrequency(be))
#> DataFrame with 6 rows and 4 columns
#>              freq       maf  callRate heterozygosity
#>         <numeric> <numeric> <numeric>      <numeric>
#> snp0001  0.450000  0.450000         1       0.633333
#> snp0002  0.333333  0.333333         1       0.466667
#> snp0003  0.500000  0.500000         1       0.600000
#> snp0004  0.816667  0.183333         1       0.233333
#> snp0005  0.333333  0.333333         1       0.333333
#> snp0006  0.800000  0.200000         1       0.266667