Signac: Footprint – R documentation

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Footprint

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
`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
`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

Signac

Analysis of Single-Cell Chromatin Data

v1.2.1

MIT + file LICENSE

Authors

Tim Stuart [aut, cre] (<https://orcid.org/0000-0002-3044-0897>), Avi Srivastava [aut] (<https://orcid.org/0000-0001-9798-2079>), Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>), Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)

Initial release

2021-05-11