1. Find the peaks with bi-directional promoters with summary statistics (peaksNearBDP). 
2. Summarize the occurrence of motifs in peaks (summarizePatternInPeaks). 
3. Add other IDs to annotated peaks or enrichedGO (addGeneIDs)The function makeVennDiagram supports 4-way venn diagram.
4. Enriched Gene Ontology (GO) terms are annotated with a list of genes which can be traced back to peaks. 
5. FAQ: http://pgfe.umassmed.edu/ChIPpeakAnno/FAQ.html.