omerwe / polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)

MIT License

89 stars 22 forks source link

Column renaming #8

Closed bschilder closed 5 years ago

bschilder commented 5 years ago

munge_polyfun_sumstats.py

It seems SNP was missing from the columns that get renamed. Added this. lines 75-77

# BMS edit:: SNP col wasn't being renamed below
    return df.rename( columns={snp_column: 'SNP', allele1_col: 'A1', allele0_col: 'A2', a1freq_col: 'MAF', bp_column: 'BP',
                 chr_column: 'CHR', info_col: 'INFO', beta_col: 'BETA', se_col: 'SE', pvalue_col: 'P', z_col: 'Z'}, errors='ignore')

omerwe commented 5 years ago

Thanks! Fixed!