AlleleFreq function

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, ...)

## Default S3 method:
AlleleFreq(object, variants, ...)

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

## S3 method for class 'StdAssay'
AlleleFreq(object, variants, ...)

## S3 method for class '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

Returns

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