Enrichment Analysis in R

Question

[Bayram Sarilmaz]

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.

[Rashedul Islam]

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.

[Bayram Sarilmaz]

Edit added to the question. Please have a look

Answer 1

[venu]

Check GeneOverlap package. It has functions to do what you need.

[Bayram Sarilmaz]

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?

[venu]

There is so called vignettes/manual/docuemntation for every R/Bioconductor package. You can find use cases in there.