MotifSetEnrichmentAnalysis: `MotifSetEnrichmentAnalysis`

Description

This analogous to Gene Set Enrichment Analysis. Instead of testing for enrichment of a geneset with a given gene set in a pathway, we are testing the enrichment of a given TF motif set against a motif set downstream of a multiple ligands. If there is enrichment, it's a sign that that ligand could drive that set of motifs.

Usage

MotifSetEnrichmentAnalysis(
  ligandTFMatrix,
  motifEnrichmentDF,
  motifColumn,
  ligands,
  statColumn,
  statThreshold,
  annotationName = "CellType",
  annotation = "none",
  numCores = 1,
  verbose = FALSE
)

Value

specDF A dataframe containing enrichment analysis results

Arguments

ligandTFMatrix: NicheNet Ligand-TF matrix
motifEnrichmentDF: Dataframe (unfiltered) from ArchR's peakAnnoEnrich step. Expected to have a column with motif names, and a column with the -log10 adjusted p-values.
motifColumn: Column name within the motifEnrichmentDF that has motif names.
ligands: Vector of ligands to test
statColumn: Column name in motifEnrichmentDF containing the statistic to test
statThreshold: Significance threshold used to select significant motif set
annotationName: Optional column name for the annotation. Default is "CellType".
annotation: Optional annotation value added to all rows of the output motif dataframe. Can be character vector or numeric. Default is "none".
numCores: The number of cores to use with multiprocessing. Default is 1.
verbose: Set TRUE to display additional messages. Default is FALSE.