I have two bed files, and I would like to know if bed file A is enriched in bed file B compared to what is expected, given the genome sizes. I found how to get a p-value for this using Fisher, at least an idea of the baseline: bedtools fisher -a testA.bed -b testB.bed -g chrom_hg19.sizes,
Now I had three questions: Is this the usual way to do enrichment of features genome-wide? My feature in bed file A does not include the sex chromosomes, while bed file B and chrom_hg19.sizes do. Would this influence the estimates? Is there a way to get a log fold change?
Thanks very much!