ATACqc: Compute scATAC-seq QC metrics

In Signac: Analysis of Single-Cell Chromatin Data

Compute scATAC-seq QC metrics

Description

Wrapper function to run ⁠fragtk qc⁠ and add the metadata to the Seurat object.

Usage

ATACqc(object, ...)

## Default S3 method:
ATACqc(
  object,
  annotations,
  fragtk.path = NULL,
  outdir = tempdir(),
  cleanup = TRUE,
  verbose = TRUE,
  ...
)

## S3 method for class 'ChromatinAssay'
ATACqc(
  object,
  annotations = NULL,
  fragtk.path = NULL,
  outdir = tempdir(),
  cleanup = TRUE,
  verbose = TRUE,
  ...
)

## S3 method for class 'Seurat'
ATACqc(
  object,
  assay = NULL,
  annotations = NULL,
  fragtk.path = NULL,
  outdir = tempdir(),
  cleanup = TRUE,
  verbose = TRUE,
  ...
)

Arguments

object	A Seurat object, ChromatinAssay object, or path to a fragment file.
...	Arguments passed to other methods
annotations	GenomicRanges::GRanges() object containing gene annotations. If NULL, attempt to extract this from the ChromatinAssay object if provided.
fragtk.path	Path to fragtk executable. If NULL, try to find fragtk automatically.
outdir	Path for output directory
cleanup	Remove output files created by fragtk
verbose	Display messages
assay	Name of assay to use. If NULL, use the default assay.

Signac documentation built on April 1, 2026, 5:06 p.m.