I am trying to represent a large (many million entries) interaction matrix between genomic loci, possibly on different chromosomes. These matrices are generally the results of 5C/Hi-C type experiments.
Q: is there an existing data structure based on IRanges that does something like that?
In essence each entry would consist of two genomic ranges, one for the source and one for the target, possibly with a frequency field showing how many times this interaction was sequenced. I used simple data frames so far, which serves the purpose, but might not be the most efficient in terms of storage.