Question: Enrichment Analysis in R
0
gravatar for Bayram Sarilmaz
14 months ago by
Bayram Sarilmaz0 wrote:

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.

ADD COMMENTlink modified 14 months ago • written 14 months ago by Bayram Sarilmaz0

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.

ADD REPLYlink modified 14 months ago • written 14 months ago by Rashedul Islam340

Edit added to the question. Please have a look

ADD REPLYlink written 14 months ago by Bayram Sarilmaz0
2
gravatar for venu
14 months ago by
venu6.3k
Germany
venu6.3k wrote:

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

ADD COMMENTlink written 14 months ago by venu6.3k

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?

ADD REPLYlink written 14 months ago by Bayram Sarilmaz0

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

ADD REPLYlink written 14 months ago by venu6.3k
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