natsuhiko/rasqual

condition specific eQTLs

gouthamatla opened this issue · 2 comments

gouthamatla commented

Hi,
I would like to know if there is any way to identify condition specific eQTLs with RASQUAL. I have two conditions from same samples. I am interested to see the eQTLs that are detected in one condition but not in other and vice-versa.

If not by RASQUAL, is there an easy way of doing it ? Any pointers would be very useful.

natsuhiko commented

Unfortunately, there is no function to properly perform conditional specific eQTL mapping with RASQUAL. You can only map eQTLs separately for those two conditions, and draw a threshold (e.g., FDR 10%) to classify a pair of eQTLs into shared, condition specific, or null for both conditions. I would recommend to use other approaches, such as MASHR, to perform a proper analysis for this purpose.

gouthamatla commented

Thanks,

I will check MASHR.