genomic coordinate in R

Question

I am working on the TxDb.Hsapiens.UCSC.hg19.knownGene data. I found that the length of the largest exon is 205012. How can I proceed to find the genomic coordinate of that exon?

If you found the maximum range with the function `max`, you might want to consider using the function `which.max` to know which one is the max. — Vincent Guillemot, Mar 14 '21 at 18:41

score 1 · Answer 1 · answered Mar 14 '21 at 18:46

1

You can use which.max() on the Granges, something like below:

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb = TxDb.Hsapiens.UCSC.hg19.knownGene
ex = exons(txdb)
ex$len = width(ex)
ex[which.max(ex$len)]

GRanges object with 1 range and 2 metadata columns:
      seqnames              ranges strand |   exon_id       len
         <Rle>           <IRanges>  <Rle> | <integer> <integer>
  [1]    chr12 102591363-102796374      + |    164764    205012
  -------
  seqinfo: 93 sequences (1 circular) from hg19 genome

answered Mar 14 '21 at 18:46

StupidWolf

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Thank you for your answer to my question – Chris7 Mar 14 '21 at 20:02
Hi @Chris7, if it indeeds solves the problem, you can consider accepting it so that others know it works – StupidWolf Mar 14 '21 at 20:03
https://meta.stackexchange.com/questions/5234/how-does-accepting-an-answer-work – StupidWolf Mar 14 '21 at 20:03

genomic coordinate in R

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