I am trying to find a p-value for enrichment of ChIP-Seq peaks from a bed file within a chromatin state from the UCSC stored in another bed file. I overlapped the two bed files using BedTools and now I have these values:
The number of ChiP-Seq peaks that overlap a chromatin state (more than one peak can overlap a chromatin state, but a specific peak belongs to only one chromatin state)= 10450
The total number of ChiP-Seq peaks = 100561
The total coverage of a chromatin state = 204652
How can I get a p-value of enrichment for the CHiP-Seq peak within the chromatin state?
This biostar answer is quite comprehensive. Personally, I had used the bedtools fisher, you'll need your list of peaks, your list of chromatin states and a file with the chromosome sizes.