Compute allele frequencies per cell — AlleleFreq • Signac

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

Value

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