Hi Aaron,
I was recently trying out PALM got into some confusion which I would like to clarify:
the wiki page mentions that the meta-data table should contain the following columns
variant derived_allele minor_AF beta pval
however, running the palm.py script with such a table gives an error. By looking into the code and the example meta-data tables from the paper supplementary seems that the SE is required and is used to calculate the p-value which is then used for filtering.
So I just wonder if my understanding is correct and I can safely change the script to evaluate the p-value from the input directly or is there something I missed.
Cheers,
Vasili
Hi Aaron,
I was recently trying out PALM got into some confusion which I would like to clarify:
the wiki page mentions that the meta-data table should contain the following columns
variant derived_allele minor_AF beta pval
however, running the palm.py script with such a table gives an error. By looking into the code and the example meta-data tables from the paper supplementary seems that the SE is required and is used to calculate the p-value which is then used for filtering.
So I just wonder if my understanding is correct and I can safely change the script to evaluate the p-value from the input directly or is there something I missed.
Cheers,
Vasili