fisher test, X test, Cramer’s V

[joscarhuguet]

I have three groups of fungal genes. These were obtained by presence and absence in non-pathogens, animal pathogens and plant-pathogens. I am trying to find any overepresented COG or pfam group in each group. Does anybody familiar which what kind of test is the best to apply, Fisher? Cramer's V? Chi test.
I am thinking to use R. Wonder if there is an specific package in R for this analysis
Thanks