Closed JohnHadish closed 4 years ago
@JohnHadish I think there might be confusion about what that option does. It doesn't select n edges, but the top n ranked edges. Some edges can have the same rank. Also, it will select each the top n ranked edges per condition as well.
I went ahead and fixed this issue so that it is no longer confusing. PR #177 has been submitted.
The
--top_n
option forkinc-filter-rank.R
does not do what the documentation says. When I set it to10000
it returned16553789
edges. There are many edges which receive identical rankings, so while the file only goes up toi rank10000
there can be many edges for a specific rank. If I select only the top 10,000 edges, I only will get to rank 192.