The Motif class

The Motif class is designed to store DNA sequence motif information, including motif PWMs or PFMs, motif positions, and metadata.

Slots

data

A feature x motif matrix. Columns correspond to motif IDs, rows correspond to features of interest (for example, genomic regions). Entries in the matrix should be 1 if the feature contains the motif and 0 otherwise.

pwm

A named list of position weight matrices

motif.names

A list containing the name of each motif

positions

A GenomicRanges::GRangesList() object containing exact positions of each motif in the genome.

meta.data

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