Fix crash, return to original number of genes with simulated cliques

Instead of using hard-coded example values, use original (larger) number
of genes set as default in initializeParams(). Crash was due to the
following two errors:
- The oldComponents simulated in R was using 1-indexing instead of
0-indexing.
- oldComponentsInput was not being correctly copied in the C++ layer
with the result that the list for each clique always started off the
same, and therefore sometimes contained indices that were out of bounds
for that clique.