[Bioc-devel] SummarizedExperiment

2014-03-20 Thread Kasper Daniel Hansen
It used to be the case that when a SummarizedExperiment was constructed, dim names was removed from the matrices in assay. One could then either use (1) assay(, withDimnames = TRUE) which ensured dim names in the return value, but implied copying of the return object because the dim names had to

Re: [Bioc-devel] restrictToSNV for VCF

2014-03-20 Thread Hervé Pagès
On 03/20/2014 05:20 PM, Hervé Pagès wrote: [...] Following that logic names(se1) also probably return colnames(se1). /\ should H. H. On Wed, Mar 19, 2014 at 1:07 PM, Vincent Carey wrote: On Wed, Mar 19, 2014 at 4:00

Re: [Bioc-devel] restrictToSNV for VCF

2014-03-20 Thread Hervé Pagès
Hi, On 03/19/2014 01:10 PM, Michael Lawrence wrote: You can apparently use 1D extraction for VCF, which is a little surprising; I learned it from restrictToSNV. This is inherited from SummarizedExperiment: > example(SummarizedExperiment) > se1 class: SummarizedExperiment dim: 200 6