how to generate/input phewas data

[Mokerina Liao]

Hi Team,

I am recently trying the pheweb package and found that it is really impressive and amazing.

Yet I am somehow confused that how to set up the PheWAS data. In the Pheweb instruction page, I couldn't find where to input the dataset for performing PheWAS.  Is there any instruction?

Thanks!

[Peter VandeHaar]

You need one file for each phenotype (ie, one file per GWAS).  Section 3 of the instructions describes what those files should be like: https://github.com/statgen/pheweb#3-prepare-your-association-files .

Then you need to make a list of the paths to those files.  Section 4 of the instructions talks about that: https://github.com/statgen/pheweb#4-make-a-list-of-your-phenotypes .

I hope that helps.  I can't tell from your post what exactly you're having trouble with.

Peter