For any set of genomic coordinates representing a genomic feature and a given state, the fold enrichment of overlap is calculated as the ratio of “the joint probability of a region belonging to the state and the feature” vs. “the product of independent marginal probability of observing the state in the genome” times “the probability of of observing the feature”, namely the ratio between the (#bases in state AND overlap feature)/(#bases in genome) and the [(#bases overlap feature)/(#bases in genome) X (#bases in state)/(#bases in genome)]. The neighborhood enrichment is computed for genomic bins around a set of single base pair anchor locations in the genome e.g. transcription start sites.
