Transcription factor footprinting analysis

Compute the normalized observed/expected Tn5 insertion frequency for each position surrounding a set of motif instances.

Usage

Footprint(object, ...)

# S3 method for class 'ChromatinAssay5'
Footprint(
  object,
  genome,
  motif.name = NULL,
  key = motif.name,
  regions = NULL,
  assay = NULL,
  upstream = 250,
  downstream = 250,
  compute.expected = TRUE,
  in.peaks = FALSE,
  overwrite = FALSE,
  verbose = TRUE,
  ...
)

# S3 method for class 'Seurat'
Footprint(
  object,
  genome,
  regions = NULL,
  motif.name = NULL,
  assay = NULL,
  upstream = 250,
  downstream = 250,
  in.peaks = FALSE,
  overwrite = FALSE,
  verbose = TRUE,
  ...
)

Arguments

object: A SeuratObject::Seurat or ChromatinAssay5 object
...: Arguments passed to other methods
genome: A BSgenome::BSgenome object or any other object supported by BSgenome::getSeq(). Do showMethods("getSeq") to get the list of all supported object types.
motif.name: Name of a motif stored in the assay to footprint. If not supplied, must supply a set of regions.
key: Key to store positional enrichment information under.
regions: A set of genomic ranges containing the motif instances. These should all be the same width.
assay: Name of assay to use
upstream: Number of bases to extend upstream
downstream: Number of bases to extend downstream
compute.expected: Find the expected number of insertions at each position given the local DNA sequence context and the insertion bias of Tn5
in.peaks: Restrict motifs to those that fall in peaks
overwrite: Overwrite existing RegionAggregation objects with the same name
verbose: Display messages

Value

Returns a SeuratObject::Seurat object