This may not be as straightforward as a one-to-one comparison, but I think it'll still be a useful exercise at first to compare effect p values of CIT results from the xQTL paper to what I get grouping by gene and considering each eQTL SNP at once (even though they may not all directly associate with each probe). I will need to:
[ ] Debug and get rosmap_cit_replication.py running on orenthal
[ ] Write up an analysis that makes as direct a comparison as possible to the results in the CIT.txt file on xQTLserve
This may not be as straightforward as a one-to-one comparison, but I think it'll still be a useful exercise at first to compare effect p values of CIT results from the xQTL paper to what I get grouping by gene and considering each eQTL SNP at once (even though they may not all directly associate with each probe). I will need to:
rosmap_cit_replication.pyrunning on orenthalCIT.txtfile on xQTLserve