Footprint {Signac}

Transcription factor footprinting analysis

Description

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

Usage

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

Value

Returns a Seurat object