[BioC] exonsBy order

[Valerie Obenchain]

Hello,

The ordering of the ranges within each list element is described on the 
man page (seen by typing ?exonsBy).

      "When using ‘exonsBy’ and ‘cdsBy’ with ‘by = "tx"’, the ranges are
      returned in the order they appear in the transcript, i.e. order by
      the splicing.exon_rank field in ‘x’'s internal database. In all
      other cases, the ranges will be ordered by chromosome, strand,
      start, and end values."

If you are using exonsBy(..., by="tx") the ranges are returned as they 
appear in the transcript. Using exonsBy(..., by="gene") will return the 
ranges ordered by chromosome, strand, start and end.

Valerie


On 04/02/2013 07:00 AM, Ido Tamir wrote:
> Hi,
> is it guaranteed that the exons within each of the GRanges resulting from exonsBy
> are sorted in ascending order?
>
> The GRangesList seems unsorted.
>
> thank you very much,
> ido
>
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