[Bioc-devel] Combining Ordinary List of GRanges Optimisation

Dario Strbenac D.Strbenac at garvan.org.au
Mon Jan 7 04:00:11 CET 2013

> Are you asking if you can rewrite your code to work faster, or are you asking if the BioC devs need to improve the code to be faster?

I was suggesting that maybe the c function for GRanges could be optimised.

> Another would be manually splitting each GRanges objects into its components: seqnames, IRanges, strand, and metadata. Then concatenate these components and build one big GRanges object.

This approach gives:

   user  system elapsed 
 63.488  11.092  74.786

which by using c was previously:

   user  system elapsed 
935.770  23.657 961.952

Thanks for the tip. I now remember using this approach at some time in the past.

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