Figure 1. Overview of the classes in the InteractionSet package.

Relevant slots of each class (i.e., data values stored in each object of the class) are labelled with a preceding “@”. ( A) The GInteractions class represents pairwise interactions between genomic regions by storing pairs of anchor indices that refer to coordinates in a GenomicRanges object. ( B) The InteractionSet class stores experimental data in an “assays” matrix where each row is an interaction and each column is a sample. Here, counts represent the number of read pairs mapped between each pair of interacting regions in each sample. ( C) The ContactMatrix class represents the interaction space as a matrix, where each cell represents an interaction between the corresponding row/column regions.