arq5x/gemini — pull request #167 by roryk (2013-07-10 15:28:58+00:00)
Title: burden testing

Hi Aaron,

I'm pull requesting this so we can talk about it before it gets merged; it adds some dependencies to GEMINI. I added a couple summaries to gemini_stats.py:

The first is --burden which just spits out how many high impact variants there are for each gene in each sample.
The second is --nonsynonymous which does the same thing, but for all non-synonymous variants, not just high-impact.
The third is --calpha which takes a list of case and control samples with --controls and --cases. It does the c-alpha test on those samples and spits out p-values for genes with variances higher than expected.

It does use pandas to aggregate the ata and scipy to calculate some of the stats; I think the difficult to install dependency is numpy though, if numpy is installed correctly pandas and scipy seem to be able to be installed without a hitch.