R/AllGenerics.R

In VariantExperiment: A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend

## #' @rdname VariantExperiment-methods
## #' @export seqAlleleFreq seqAlleleCount seqMissing seqNumAllele

## SeqArray: seqAlleleFreq seqAlleleCount seqMissing seqNumAllele
setGeneric("seqAlleleFreq",
           function(gdsfile, ref.allele=0L, minor=FALSE, .progress=FALSE,
                    parallel=seqGetParallel(), verbose=FALSE)
               standardGeneric("seqAlleleFreq"),
           useAsDefault=SeqArray::seqAlleleFreq,
           signature="gdsfile")
setGeneric("seqAlleleCount",
           function(gdsfile, ref.allele=0L, minor=FALSE, .progress=FALSE,
                    parallel=seqGetParallel(), verbose=FALSE)
               standardGeneric("seqAlleleCount"),
           useAsDefault=SeqArray::seqAlleleCount,
           signature="gdsfile")
setGeneric("seqMissing",
           function(gdsfile, per.variant=TRUE, .progress=FALSE,
                    parallel=seqGetParallel(), verbose=FALSE)
               standardGeneric("seqMissing"),
           useAsDefault=SeqArray::seqMissing,
           signature="gdsfile")
setGeneric("seqNumAllele",
           function(gdsfile)
               standardGeneric("seqNumAllele"),
           useAsDefault=SeqArray::seqNumAllele,
           signature="gdsfile")