Compute allele frequencies per cell

Collapses allele counts for each strand and normalize by the total number of counts at each nucleotide position.

AlleleFreq(object, ...)

# S3 method for default
AlleleFreq(object, variants, ...)

# S3 method for Assay
AlleleFreq(object, variants, ...)

# S3 method for Seurat
AlleleFreq(object, variants, assay = NULL, new.assay.name = "alleles", ...)

Arguments

object	A Seurat object, Assay, or matrix
...	Arguments passed to other methods
variants	A character vector of informative variants to keep. For example, c("627G>A","709G>A","1045G>A","1793G>A").
assay	Name of assay to use
new.assay.name	Name of new assay to store variant data in

Value

Returns a Seurat object with a new assay containing the allele frequencies for the informative variants.