Finding the nearest n genes from a genomic loci
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ssabri ▴ 20
@ssabri-9464
Last seen 4.0 years ago

I am aware of the nearest() function but I believe this is limited to finding the nearest single gene to a loci. Is there a way to compute the n nearest genes for a genomic loci? I ultimately want to do this for a genomicranges object that is segmented into approximately 3 million non-overlapping ranges/bins. These loci are defined by binning a chromosome into 200bp windows. Thank you! 

 

 

genomicranges • 728 views
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@michael-lawrence-3846
Last seen 2.3 years ago
United States

There is a hidden function GenomicRanges:::findKNN() that might do the trick. It's largely untested so let me know whether it works.

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