Signac: FindMotifs – R documentation

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FindMotifs

Description

Find motifs over-represented in a given set of genomic features. Computes the number of features containing the motif (observed) and compares this to the total number of features containing the motif (background) using the hypergeometric test.

Usage

FindMotifs(
  object,
  features,
  background = 40000,
  assay = NULL,
  verbose = TRUE,
  ...
)

Arguments

`object`	A Seurat object
`features`	A vector of features to test for enrichments over background
`background`	Either a vector of features to use as the background set, or a number specify the number of features to randomly select as a background set. If a number is provided, regions will be selected to match the sequence characteristics of the query features. To match the sequence characteristics, these characteristics must be stored in the feature metadata for the assay. This can be added using the `RegionStats` function. If NULL, use all features in the assay.
`assay`	Which assay to use. Default is the active assay
`verbose`	Display messages
`...`	Arguments passed to `MatchRegionStats`.

Value

Returns a data frame

Examples

de.motif <- head(rownames(atac_small))
bg.peaks <- tail(rownames(atac_small))
FindMotifs(
  object = atac_small,
  features = de.motif,
  background = bg.peaks
)

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