Find enriched ontology terms — EnrichedTerms • Signac

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.