[Bioc-devel] Fast accessor for assay names of SummarizedExperiment

Martin Morgan mtmorgan at fredhutch.org
Wed Nov 26 03:36:30 CET 2014

On 11/25/2014 04:46 PM, Peter Hickey wrote:
> Hi Martin,
> Accessing the names of the assays in a SummarizedExperiment object is very slow when doing this by what seems that natural way of names(assay(se)). I now see that it should be done by names(assay(se, withDimnames = FALSE). But I was only able to figure this out by some googling which led me to https://stat.ethz.ch/pipermail/bioc-devel/2014-May/005724.html - perhaps it's worth including some documentation on the implications of 'withDimnames' when accessing the assays slot (I still don't fully understand it).
> I also noticed that Kasper implemented an assayNames() helper function in his bsseq package that is ever so slightly faster. Do others think a general assayNames() helper function is worth including in GenomicRanges?
> Benchmarks at https://gist.github.com/PeteHaitch/346b924e3eca8c3cfade

Hi Pete -- I added assayNames and assayNames<- to GenomicRanges, and updated 
bsseq (hope that's ok, Kasper?) to implement a method on the generic; my 
implementation does not use direct slot / field access, so is a lot faster but 
not the fastest.

I also documented the consequences of withDimnames=FALSE.



> Thanks,
> Pete
> --------------------------------
> Peter Hickey,
> PhD Student/Research Assistant,
> Bioinformatics Division,
> Walter and Eliza Hall Institute of Medical Research,
> 1G Royal Parade, Parkville, Vic 3052, Australia.
> Ph: +613 9345 2324
> hickey at wehi.edu.au
> http://www.wehi.edu.au
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