Hi, there

I am using the extendRegions function to get the extended GRanges, however, it automatically ignores the strand information.  

For example:

> genes
GRanges object with 33602 ranges and 1 metadata column:
            seqnames        ranges strand |     gene_id
               <Rle>     <IRanges>  <Rle> | <character>
  AT1G01010        1     3631-5899      + |   AT1G01010
  AT1G01020        1     5928-8737      - |   AT1G01020

After using the function, we obtained followings:

extendRegions(genes,extend.start = 1000)
GRanges object with 33602 ranges and 1 metadata column:
            seqnames        ranges strand |     gene_id
               <Rle>     <IRanges>  <Rle> | <character>
  AT1G01010        1     2631-5899      + |   AT1G01010
  AT1G01020        1     4928-8737      - |   AT1G01020

Obviously, the first gene's range was correctly extended, but the second gene was wrong. It should be  5928-9737. How to fix it ? Thanks

Hi @wuzefeng2008

The region management functions in regioneR does not take into account strand information at the moment. It's in our TODO list and strand management should be added by next Bioconductor release.

Bernat