Question: P-value for enrichment of ChIP-Seq peaks within a genomic annotation
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gravatar for User 7754
3.8 years ago by
User 7754230
United Kingdom
User 7754230 wrote:

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 • 2.1k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by User 7754230

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.

ADD REPLYlink written 3.8 years ago by Fidel1.9k
0
gravatar for dally
3.8 years ago by
dally180
United States
dally180 wrote:

Have you thought about the phyper function in R?

ADD COMMENTlink written 3.8 years ago by dally180

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)

ADD REPLYlink written 3.8 years ago by User 7754230

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.

ADD REPLYlink written 3.8 years ago by dally180

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?

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by User 7754230
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