For ORA results, clusterProfiler provides geneRatio (ratio of input genes that are annotated in a term) and BgRatio (ratio of all genes that are annotated in this term). However, other concepts are widely used to help in interpreting enrichment results, such as the rich factor and fold enrichment. A rich factor is defined as the ratio of input genes (e.g., DEGs) that are annotated in a term to all genes that are annotated in this term. The fold enrichment is defined as the ratio of the frequency of input genes annotated in a term to the frequency of all genes annotated to that term, and it is easy to calculate by dividing geneRatio by BgRatio. Here, as an example, we used the mutate verb to create a new column of richFactor based on information available in the clusterProfiler output.ego3 <- mutate(ego, richFactor = Count / as.numeric(sub("/\\d+", "", BgRatio)))
