Fix subMgsaSets()

subMgsaSets() method is very handy when set enrichment needs to be checked within the constrained pool of genes.
The update fixes some issues in the current implementation:
 - instead of the item ids (i.e. Entrez Gene IDs) the user has to provide item indices
 - item and set annotations are not preserved
 - in the subsetted MgsaSets the original item ids are replaced by item indices