I am currently working on a project with a binary outcome, and need to report beta coefficients (representing the log-odds increase per copy of the minor allele), confidence intervals, and odds ratios for each variant. I am using a SeqVarGDSClass object with a SeqVarIterator, and have run fitNullModel and assocTestSingle with no problems. Since my outcome is binary and I am using the “family=binomial” option in fitNullModel, the association test produces Score test statistics only.
My question is – do you know if it is possible to get beta coefficients and standard errors for an additive model with a binary outcome using GENESIS?
You have two options for calculating betas for binary outcomes.
Option 1) refit the null model including the genotypes for the variant of interest as a covariate. This is a good option if you only need betas for a small number of variants. You can use SeqVarTools::altDosage to get the alternate allele dosage for a given variant or set of variants.