oddRatio: Odd Ratio

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

Odd Ratio

Description

This function computes the odd ratio of observed vs expected events. The odd ratio (OR) is computed as (observedTrue/observedFalse) x (expectedFalse/expectedTrue), while the confidence interval (CI) is computed as exp(log(or) + c(-1,1) x 1.96 x sqrt(1/observedTrue + 1/observedFalse + 1/expectedTrue + 1/expectedFalse)). If any of the four input values is 0, then a modified Haldane-Anscombe (mHA) correction is applied, adding 0.5 to all values. The result of the fisher.test R function is also reported, which uses the Conditional Maximum Likelihood Estimate (CMLE) and can report slightly different OR and CI

Usage

oddRatio(observedTrue, observedFalse, expectedTrue, expectedFalse)

Arguments

observedTrue	count of observed true cases
observedFalse	count of observed false cases
expectedTrue	count of expected true cases
expectedFalse	count of expected false cases

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.