Saturday, July 7, 2012

Fwd: significance of overlap - Google Groups

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significance of overlap - Google Groups: Re: [bedtools-discuss] significance of overlap

Hi Bogdan,

Currently, bedtools itself does not have a single command to do this.  Instead, one would measure significance using Monte Carlo simulations by writing a script to shuffle (shuffleBed) files many (e.g., 1e3, or more) times and compare the observed intersection to the expected (e.g., max if seeking a P-value or median if seeking an enrichment score) intersection based on shuffling.

Fortunately, Ryan Dale has written some really nice scripts for this in the pybedtools package that we collaborate on.  See this thread for details.
https://groups.google.com/group/bedtools-discuss/browse_thread/thread/9518a38ca04478fd

Cheers,
Aaron

(Original Post by Aaron: significance of overlap - Google Groups.)