comparing 2 long BED files in R in an efficient way
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Bogdan ▴ 620
@bogdan-2367
Last seen 14 days ago
Palo Alto, CA, USA

Dear all,

please would you advise about an efficient R code to solve the following problem :

-- given a BED file with the variant coordinates (> 10 000 entries) : let's call the file A

-- and a BED file with the gene coordinates (>50 000 genes) :  let's call the file B

what is most efficient way to write the comparison in R, between file A and file B, and append the gene from file B to the file A, if there is an intersection of genomic coordinates ? thanks a lot !

 

bogdan

bed vcf • 386 views
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@genomic_region-13050
Last seen 7 months ago

Cross posted: https://www.biostars.org/p/324164/

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