EnrichedTerms: Find enriched ontology terms

In Signac: Analysis of Single-Cell Chromatin Data

Find enriched ontology terms

Description

Run ontology term enrichment testing on differential features for each of the identity classes. Runs fgsea::fgsea() on differential testing results from each identity class.

Usage

EnrichedTerms(
  object,
  terms,
  group.by = NULL,
  assay = NULL,
  var.features = TRUE,
  scoreType = "std",
  top.n = NULL,
  verbose = TRUE,
  ...
)

Arguments

object	A Seurat object.
terms	Ontology term list. The name of each element in the list should be an ontology term, and the list elements a vector of feature names present in the assay.
group.by	Name of grouping variable to use. If NULL, use the active cell identities.
assay	Name of assay to use. If NULL, use the default assay.
var.features	Subset to only variable features for ontology term enrichment.
scoreType	scoreType parameter for fgsea::fgseaSimple(). Options are "std", "pos", "neg" (two-tailed or one-tailed tests).
top.n	Number of top enriched terms to retain for each set of cells. If NULL, retain all terms.
verbose	Display messages.
...	Additional arguments passed to Seurat::FindMarkers()

Value

Returns a named list of dataframes. Each element of the list contains a dataframe with the term enrichment results for an identity class.

Signac documentation built on April 1, 2026, 5:06 p.m.