Identify mitochondrial variants

Identify mitochondrial variants present in single cells.

Usage

IdentifyVariants(object, ...)

# Default S3 method
IdentifyVariants(
  object,
  refallele,
  stabilize_variance = TRUE,
  low_coverage_threshold = 10,
  verbose = TRUE,
  ...
)

# S3 method for class 'Assay'
IdentifyVariants(object, refallele, ...)

# S3 method for class 'StdAssay'
IdentifyVariants(object, refallele, ...)

# S3 method for class 'Seurat'
IdentifyVariants(object, refallele, assay = NULL, ...)

Arguments

object

A Seurat object

...

Arguments passed to other methods

refallele

A dataframe containing reference alleles for the mitochondrial genome.

stabilize_variance

Stabilize variance

low_coverage_threshold

Low coverage threshold

verbose

Display messages

assay

Name of assay to use. If NULL, use the default assay.

Value

Returns a dataframe

Examples

if (FALSE) { # \dontrun{
data.dir <- "path/to/data/directory"
mgatk <- ReadMGATK(dir = data.dir)
variant.df <- IdentifyVariants(
  object = mgatk$counts,
  refallele = mgatk$refallele
)
} # }