FindMotifs function

FindMotifs

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.

FindMotifs(
  object,
  features,
  background = 40000,
  assay = NULL,
  verbose = TRUE,
  p.adjust.method = "BH",
  ...
)

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
• p.adjust.method: Multiple testing correction method to be applied. Passed to p.adjust.
• ...: Arguments passed to MatchRegionStats.

Returns

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
)