How to perform Fisher's exact test between two gene lists for a particular gene in R?

Question

[Vasu]

Hello Everyone,

I have two gene lists with sample, gene, chromosome, mutation_type, start, end, codon columns. Want to perform Fishers test between two gene lists for a particular gene eg: MAP3K1. Can anyone tell me how can I perform this in R?

Thank you

[Tom_L]

Are you talking about the FET implemented in the fisher.text() function? Can you please post an example so we can understand what kind of data you want to analyze?

[Vasu]

For eg: I want see for MAP3K1. Could you please tell how to see it is wildtype or mutant? And then after that I want to perform fisher.test function.

             MAP3K1 
            wt  mutant
Genelist1    x    x
Genelist2    x    x

[Tom_L]

If you can summarize your dataframes into two columns "MAP3K1" (containing values "wt" and "mutant") and "LIST" ("list1" and "list2") then you could use table() to automatically generate contingency matrices. I don't know how easy this will be since I don't know the architectures of your dataframes. I guess an apply() function could help you to get the information you need.

Answer 1

[sysbiocoder]

You can use Gene Overlap package in R

https://bioconductor.org/packages/release/bioc/html/GeneOverlap.html