Skip to content
Prev 3964 / 21312 Next
Original Raw

[Bioc-devel] Combining Ordinary List of GRanges Optimisation

Ryan 
Hi Dario Strbenac,

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? As a 
first test, I would try a few alternatives to see if they are 
significantly faster. One would be "unlist(GRangesList(blockRanges))". 
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. Try both of these 
approaches and see if either one makes things faster.

Alternatively, give me some code to generate a list of GRanges similar 
in size to your blockRanges object, and I'll test them myself.

-Ryan Thompson
On 01/06/2013 06:00 PM, Dario Strbenac wrote:

Thread (10 messages)

Dario Strbenac Combining Ordinary List of GRanges Optimisation Jan 6 Ryan Combining Ordinary List of GRanges Optimisation Jan 6 Dario Strbenac Combining Ordinary List of GRanges Optimisation Jan 6 Hahne, Florian Combining Ordinary List of GRanges Optimisation Jan 7 Michael Lawrence Combining Ordinary List of GRanges Optimisation Jan 7 Ryan Combining Ordinary List of GRanges Optimisation Jan 7 Michael Lawrence Combining Ordinary List of GRanges Optimisation Jan 7 Hervé Pagès Combining Ordinary List of GRanges Optimisation Jan 8 Michael Lawrence Combining Ordinary List of GRanges Optimisation Jan 8 Hervé Pagès Combining Ordinary List of GRanges Optimisation Jan 8