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!
Martin
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
hic...@wehi.edu.au
http://www.wehi.edu.au
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