2.5 years ago by
I will give an example to explain this that helped me understand it. I also was looking for the answer and Guangchuang link helped.
Let is suppose I have a collection of genesets called : HALLMARK
Now let is suppose there is a specific geneset there called: E2F_targets
M = size of the geneset (eg size of the E2F_targets); (is the number of genes within that distribution that are annotated (either directly or indirectly) to the node of interest).
N = size of all of the unique genes in the collection of genesets (example the HALLMARK collection); (is the total number of genes in the background distribution (universe)
GeneRatio is k/n.
k = size of the overlap of 'a vector of gene id' you input with the specific geneset (eg E2F_targets), only unique genes; (the number of genes within that list n, which are annotated to the node.
n = size of the overlap of 'a vector of gene id' you input with all the members of the collection of genesets (eg the HALLMARK collection),only unique genes; is the size of the list of genes of interest