P-value for enrichment of ChIP-Seq peaks within a genomic annotation
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5.5 years ago
User 7754 ▴ 250

Hi,

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?

Thank you

ChIP-Seq • 2.8k views
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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.

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5.5 years ago
dally ▴ 190

Have you thought about the phyper function in R?

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Hi and thanks for the reply!

I have, but I am not sure what I would use for the totals including the non-overlapping peaks and annotations, would this be correct?

phyper(10450, 100561, 100561+204652, 204652-100561)
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Probability of gene list overlap

See if this helps you, I'd give you specifics but I'm not comfortable enough with my knowledge of this function to do that.

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Thanks this helps, but I am still confused about what our k would be, if we consider the number of ChiP-Seq peaks:

q=10450-1, m=100561, n=204652, k=204652?

Also would it not be important to consider that more than one ChIP peak can overlap each chromatin state?

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