How to interpret logistic interaction results from plink2 output?
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14 months ago
aj • 0

Hi,

I've run gwas logistic regression on UKBio data using plink2 geneXenvironment interaction with HB category. The results output look like this for example:

CHROM  POS   ID              REF  ALT  A1  FIRTH?  TEST          OBS_CT  OR    LOG(OR)_SE   Z_STAT  P      ERRCODE

22      160...       rs587XX     C       A       A       N       ADD             2...         0.21   4.36                 -0.351   0.72
22      160...       rs587XX     C       A       A       N       HBcat           2...         3.87   0.06                  21.27   1.86e-100
22      160...       rs587XX     C       A       A       N       ADDxHBcat  2...        1.30    2.38                  0.11    0.911


How can I combine all of the interaction terms and main SNP effects to get HB-category-specific ORs for each SNP? Can I even do it with the output given or do I need the beta coefficients?

Any help is appreciated,

AJ

SNP plink GWAS interaction logistic • 431 views
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Please elaborate some more on what you want to do, and please show the command(s) that you used to generate the current output. Please elaborate on "HB-category-specific ORs"