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MRCIEU / PHESANT

PHESANT - PHEnome Scan ANalysis Tool (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank
MIT License
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phenofile preparation #4

Closed Conxz closed 5 years ago

Conxz commented 5 years ago

Is there any trick/quick way for preparing the phenofile from the UKB data file? I think some edits should be done before input the ukbiobank .tab file to phenomeScan.r. Renameing variable name into the format 'x[varid][instance][array]' is the only edit? Thanks.

Conxz commented 5 years ago

to answer my own question, several notes that might be useful:

  1. rename variable name into the format 'x[varid][instance][array]'
  2. remove redundant columns if you are using merged outputs from multiple .tab files, such as f.eid_x, f.eid_y (just keep one of them)
louise commented 5 years ago

Thanks for your question, and answering it. Yes, the column name format should be exactly as stated in the documentation.

Best wishes, Louise