Footprint function

Transcription factor footprinting analysis

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

Footprint(object, ...)

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

Arguments

• object: A Seurat or ChromatinAssay object
• ...: Arguments passed to other methods
• genome: A BSgenome object or any other object supported by 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
• verbose: Display messages

Returns

Returns a Seurat object