Compute scATAC-seq QC metrics

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

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.