AlleleFreq {Signac}

Compute allele frequencies per cell

Description

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

Usage

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.