The Motif class

A sparse, binary, feature x motif matrix. Columns correspond to motif IDs, rows correspond to genomic features (peaks or bins). Entries in the matrix should be 1 if the genomic feature contains the motif, and 0 otherwise.

A named list of position weight matrices

A list containing the name of each motif

A dataframe for storage of additional information related to each motif. This could include the names of proteins that bind the motif.