Question: Reference allele effect allele and beta calculation
gravatar for papriscope
9 months ago by
papriscope0 wrote:

This is a simple stats question, I'm a newbie and learning and I just want to make sure I'm not missing some step.

If I have summary statistics for various SNPs with betas given, and I wish to 'flip' so to say the reference / effect alleles,

  1. is it simply flipping the sign of the beta? and then calculating the OR = exp(beta), 95%CI = exp(beta+1.96*SE) or exp(beta-1.96*SE) like I would with any categorical variable switching correct.
  2. I'm using the z-score/ normal distribution to generate the confidence interval, is that okay? or should I be aware of something?

So for example if the Ref/Effect

A/T beta = -0.23
SE =0.16

T/A beta= 0.23
OR=1.25 (95% CI 0.91-1.72)

Thank you!

statistics gwas • 289 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 9 months ago by papriscope0
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