AlleleFreq: Compute allele frequencies per cell

In Signac: Analysis of Single-Cell Chromatin Data

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.

Signac documentation built on Sept. 11, 2024, 9:30 p.m.