I have two lists of cancer genes, the genes of list-1 belong to category A, while the genes in list-2 belong to category B. I would like to perform an enrichment analysis to check whether or not category A has a enrichment of cancer genes.
Some genes are present in both categories A & B, so I think Fisher's exact test does not work in this case.
Any suggestions of other possible methods? any way to do this in R?
EDIT
So I want to do enrichment of category A, and have a set of genes that are enriched.
Check GeneOverlap package. It has functions to do what you need.
Thanks for your answer! Could you please explain a bit more on how to use this package to end up with a set of genes that are enriched for category A?
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You might need to rephrase this line " I would like to perform an enrichment analysis to check whether or not category A has a enrichment of cancer genes.". Do you want enrichment of category A over category B?
You can also check this: Statistical significance of the overlap between two groups of genes.
Edit added to the question. Please have a look