@marichards @CoryFunk,
I just added two new methods to MotifDb 1.19.3
mapMotifToTranscriptionFactorGeneSymbol(object, motifs, mode)
mapTranscriptionFactorGeneSymbolToMotif(object, geneSymbols, mode)
where mode is direct, indirect, both - from the metadata and/or tfClass (the european truck - whose tsv file is now in extdata/. unit tests and methods are stubbed in. design is open to your review.
I propose that each method return a data frame with tfGene, motif, source, pmid columns.
zzz.R now filters extdata filenames at load time, using only the .RData files to build its big datastore, allowing us to put other data (such as tbl.tfClass.tsv) in extdata/.