Gene set size?

[robinpaul85]

What does the column geneset_size actually represent in the output ? I had initially thought it is the total number of genes that are present in a given geneset. But the value is substantially lower than this number. Can you please explain?

[terynin]

The geneset_size is the intersection of that term's gene set and the input signatures list of genes. So it can be much smaller than that terms actual gene set if your signature gene's do not overlap much with it. You can see that this happens in the function strip_gene_set on line 86 of init.py. Hoped this helped.