Get Effect-Allele Frequencies

Extract the directional effect-allele (A1) frequency vector for a QtlDataset. Unlike getMaf, the value is not folded to the minor allele: it is the frequency of the dosage-counted allele (A1, the effect allele), matching the allele the marginal effect sizes and the fine-mapping af column report.

Usage

getAf(x, ...)

# S4 method for class 'QtlDataset'
getAf(x, traitId = NULL, region = NULL, cisWindow = NULL, samples = NULL, ...)

Arguments

x

A QtlDataset object.

...

Class-specific selection arguments (e.g., traitId, region, cisWindow, samples for QtlDataset).

Value

Named numeric vector of effect-allele frequencies (names are variant IDs), or an empty vector when no variants are selected.