Hi,

I would like to compute mutation co-occurence and exclusivity analysis. My first idea was to performed a fisher exact test. But after doing some litterature research there are already some tools to compute mutation mutual exclusivity that takes into account overall tumor-specific alterations . Example : http://ccb.nki.nl/software/discover/

However these tools compute mutual exclusivity . Is there some tools for co-occurence that takes into account tumor-specific alterations ?

Thank you

Edit

Looking more in detail the discover package you can do both mutual exclusive and co-occurence by modifying the alternative parameter in the pairwise.discover.test() function. By default alternative="less" and computes exclusivity. Simply modifying to alternative="greater" computes co-occurence