CallPeaks: Call peaks

Description

Call peaks using MACS. Fragment files linked to the specified assay will be used to call peaks. If multiple fragment files are present, all will be used in a single MACS invocation. Returns the .narrowPeak MACS output as a GRanges object.

Usage

CallPeaks(object, ...)
# S3 method for Seurat
CallPeaks(
  object,
  assay = NULL,
  group.by = NULL,
  idents = NULL,
  macs2.path = NULL,
  broad = FALSE,
  format = "BED",
  outdir = tempdir(),
  fragment.tempdir = tempdir(),
  combine.peaks = TRUE,
  effective.genome.size = 2.7e+09,
  extsize = 200,
  shift = -extsize/2,
  additional.args = NULL,
  name = Project(object),
  cleanup = TRUE,
  verbose = TRUE,
  ...
)
# S3 method for ChromatinAssay
CallPeaks(
  object,
  macs2.path = NULL,
  outdir = tempdir(),
  broad = FALSE,
  format = "BED",
  effective.genome.size = 2.7e+09,
  extsize = 200,
  shift = -extsize/2,
  additional.args = NULL,
  name = "macs2",
  cleanup = TRUE,
  verbose = TRUE,
  ...
)
# S3 method for Fragment
CallPeaks(
  object,
  macs2.path = NULL,
  outdir = tempdir(),
  broad = FALSE,
  format = "BED",
  effective.genome.size = 2.7e+09,
  extsize = 200,
  shift = -extsize/2,
  additional.args = NULL,
  name = "macs2",
  cleanup = TRUE,
  verbose = TRUE,
  ...
)
# S3 method for default
CallPeaks(
  object,
  macs2.path = NULL,
  outdir = tempdir(),
  broad = FALSE,
  format = "BED",
  effective.genome.size = 2.7e+09,
  extsize = 200,
  shift = -extsize/2,
  additional.args = NULL,
  name = "macs2",
  cleanup = TRUE,
  verbose = TRUE,
  ...
)

Value

Returns a GRanges object

Arguments

object: A Seurat object, ChromatinAssay object, Fragment object, or the path to fragment file/s.
...: Arguments passed to other methods
assay: Name of assay to use
group.by: Grouping variable to use. If set, peaks will be called independently on each group of cells and then combined. Note that to call peaks using subsets of cells we first split the fragment file/s used, so using a grouping variable will require extra time to split the files and perform multiple MACS peak calls, and will store additional files on-disk that may be large. Note that we store split fragment files in the temp directory (tempdir) by default, and if the program is interrupted before completing these temporary files will not be removed. If NULL, peaks are called using all cells together (pseudobulk).
idents: List of identities to include if grouping cells (only valid if also setting the group.by parameter). If NULL, peaks will be called for all cell identities.
macs2.path: Path to MACS program. If NULL, try to find MACS automatically.
broad: Call broad peaks (--broad parameter for MACS)
format: File format to use. Should be either "BED" or "BEDPE" (see MACS documentation).
outdir: Path for output files
fragment.tempdir: Path to write temporary fragment files. Only used if group.by is not NULL.
combine.peaks: Controls whether peak calls from different groups of cells are combined using GenomicRanges::reduce when calling peaks for different groups of cells (group.by parameter). If FALSE, a list of GRanges object will be returned. Note that metadata fields such as the p-value, q-value, and fold-change information for each peak will be lost if combining peaks.
effective.genome.size: Effective genome size parameter for MACS (-g). Default is the human effective genome size (2.7e9).
extsize: extsize parameter for MACS. Only relevant if format="BED"
shift: shift parameter for MACS. Only relevant if format="BED"
additional.args: Additional arguments passed to MACS. This should be a single character string
name: Name for output MACS files. This will also be placed in the name field in the GRanges output.
cleanup: Remove MACS output files
verbose: Display messages

Details

See https://macs3-project.github.io/MACS/ for MACS documentation.

If you call peaks using MACS2 please cite: tools:::Rd_expr_doi("10.1186/gb-2008-9-9-r137")