The OR value

[chaolv123]

In article"Functional Genomic Landscape of Acute Myeloid Leukemia", Fig 1. The plot involved OR value, I wonder How can they get the OR value using DISCOVER

[scanisius]

I cannot tell you how they obtained the OR value in that paper. It is not a feature that the DISCOVER package provides. As a possible alternative, if you want some measure of effect size, you could compute the observed over expected ratio. You can do so with the following code.

expected <- events$bg[gene1, ] %*% events$bg[gene2, ]
observed <- events$events[gene1, ] %*% events$events[gene2, ]
observed / expected

where events is a fitted discover.matrix object. The ratio will be < 1 for mutual exclusivity and > 1 for co-occurrence.