MotifSetEnrichmentAnalysis {MOCHA}

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
)

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.

Value

specDF A dataframe containing enrichment analysis results