I am trying to test for over-representation of a set of overlapped chip-seq peaks between constitutive exons and alternatively spliced exons.
I have a bed file that contains my overlapped chip peaks, a bed file that contains constitutive exons and a bed file that contains alternatively spliced exons (generated using a custom script provided by some authors of a paper). I am interested in running a statistical test that tells me whether my overlapped peaks are over-represented / enriched in my constitutive exon file, or alternatively spliced exon file individually.
I thought about running a hypergeometric test using the phyper function in R. But I'm not quite sure what numbers I would use specifically.
I also attempted to use the bedtools fisher test by using my overlapped chip-seq peak file and testing that against my con exon file and then my alt exon file seperately. This returned a p-value of 0 for both which I guess doesn't make much sense (though I am not very math-oriented). I mostly work on wet-lab stuff as an assistant.
Any help is appreciated.