Compute scATAC-seq QC metrics — ATACqc • Signac

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 'Fragment2'
ATACqc(
  object,
  annotations,
  fragtk.path = NULL,
  outdir = tempdir(),
  cleanup = TRUE,
  verbose = TRUE,
  ...
)

# S3 method for class 'ChromatinAssay5'
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,
  suffix = ".atacqc",
  ...
)

Arguments

object: A SeuratObject::Seurat object, ChromatinAssay5 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 ChromatinAssay5 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.
suffix: Suffix to append to the names of QC metric columns that already exist in the object metadata, to avoid overwriting them. For example, if a FRiP column computed by FRiP() is already present, the promoter-based FRiP metric computed here will instead be stored as FRiP<suffix>. Set to NULL to disable this behavior and allow existing columns to be overwritten.

Value

When run on a SeuratObject::Seurat object, returns the input object with per-cell QC metrics added to the cell metadata. When run on a ChromatinAssay5, Fragment2, or path to a fragment file, returns a data.frame of per-cell QC metrics with cell barcodes as row names. Column names correspond to the metrics produced by fragtk qc.