Calculating Log of the odds (LOD)

Question

[Matteo]

Hi all!

How can I estimate LOD scores for a phenotypic trait? Is it possible to calculate it from the association files created in GEMMA?

Thank you in advance!

Answer 1

[Kevin Blighe]

The log of the odds [ratio] can be calculated from a 2 x 2 contingency table of genotype counts of the major and minor allele, or from the odds ratio itself.

I have calculations here: SNP dataset and Z Score

Note that, in my calculations, I use natural log to calculate the Log of the Odds Ratio (Log OR); however, LOD seems to be log base 10 of the odds ratio.

If, from GEMMA, you only have the beta coefficient, then you can calculate the Odds Ratio from this by exponentiating it - the odds ratio is the exponent of the beta coefficient (effect size).

Ciao,

Kevin