How to do simple Fisher' exact test for overlapped genomic interval in R?
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@jurat-shahidin-9488
Last seen 3.9 years ago
Chicago, IL, USA

I used findOverlap() function that takes two bed file as argument to check overlapped genomic interval. this function truly returned bunch of overlapped interval. Now I want to know what's combined p-value of these overlapped interval by using Fisher' exact test. What's the simplest approach for this case? Thanks all

test fisher exact r findoverlapsofpeaks • 2.0k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 5 months ago
China/Guangzhou/Southern Medical Univer…

you can't simply apply fisher's exact test as the population is unknown.

 

see https://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html#overlap-significant-testing

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To calculate the combined p-value of overlapped genomic intervals, you can use Fisher's exact test. Merge the overlapping intervals into non-overlapping regions. You can use a tool like bedtools merge or bedops to do this. The resulting regions will represent the non-redundant genomic intervals that are covered by the original intervals. How to do simple Fisher' exact test for overlapped genomic interval in R? bitlife

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