This commit reflects changes after Bioc reviewer's comments.
1. Add collate to DESCRIPTION.
2. Restructure code so that all class definitions, all generics, accessors and methods of each class are in separate files. The original R files are deleted.
3. In the data file, change gene symbols to Ensembl IDs instead.
4. Add more prose of rationale to the vignette. Add a new heatmap about Jaccard index.