Test the enrichment of a given TF motif set against a motif set downstream of multiple ligands
Source:R/MotifSetEnrichmentAnalysis.R
MotifSetEnrichmentAnalysis.Rd
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 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
)
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.