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