IdentifyVariants: Identify mitochondrial variants

In Signac: Analysis of Single-Cell Chromatin Data

Identify mitochondrial variants

Description

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

## Not run: 
data.dir <- "path/to/data/directory"
mgatk <- ReadMGATK(dir = data.dir)
variant.df <- IdentifyVariants(
  object = mgatk$counts,
  refallele = mgatk$refallele
)

## End(Not run)

Signac documentation built on Nov. 8, 2023, 5:07 p.m.