Footprint: Transcription factor footprinting analysis

In timoast/signac: Analysis of Single-Cell Chromatin Data

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

timoast/signac documentation built on Jan. 1, 2023, 7:39 a.m.