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jaamarks / jaamarks_notebooks

Collection of various projects and procedures documented with Jupyter notebooks.
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eMERGE GWAS #7

Closed jaamarks closed 5 years ago

jaamarks commented 5 years ago

Revisiting the eMERGE GWAS for Categorical FTND. Originally I did not include an age variable as a covariate in the model. We are going back and looking into this.

Originally I used the variable from the phenotype file from dbGaP called Age_First_Cataract_Diagnosis. This was wrong. I should have used the variable px010101_age from the stata phenotype file. The reason that I involved the phenotype file from dbGaP was because I needed the sex information.

jaamarks commented 5 years ago
name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_addA1 sebeta_SNP_addA1 chi2_SNP_add
5:167394595 T C 0.12684 0.12684 0.97018 0.80427 730 0.131206 5 167394595 -0.0235898 0.0524592 0.204423
jaamarks commented 5 years ago

All finished on this from. See GitHub issue #66.