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 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
