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precimed / pleiofdr

Pleiotropy-informed conditional and conjunctional false discovery rate
GNU General Public License v3.0
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No pvalue from ldsc #6

Closed XaviFar closed 4 years ago

XaviFar commented 4 years ago

In the python_convert there is the options to convert LDSC results from munge into mat files, but when I try to run the pleioFDR it returns an error saying that there is no p-value column. Is there a way to solve this?

thanks

ofrei commented 4 years ago

@XaviFar Good point! I've added sumstats.py pvalue --sumstats <input> --out <output> - this command will add PVAL column from Z column. If Z is not available it will search for BETA and SE, and assume Z=BETA/SE to calculate PVAL. I haven't got time to test this thoroughly, please let me know if you see any issues!

XaviFar commented 4 years ago

Awesome! Thanks for the fast solution.