Added code to write all genes in GSEA gene set hits to xls files.  Also
fixed bug in clarke_mappings.txt file.  The bug was that the names of a
few genes were changed to dates when they were viewed in excel (e.g. the
gene MARCH1).  This wouldn't have affected any analysis, as I always use
Entrez ID, but some files still have incorrect gene names.  I also fixed
a bug which was calling the merge function from the wrong library, so I
added merge <- base::merge at the top of some scripts.