[Bioc-devel] GenomicRanges: Seqinfo indexing with non-existing key
julian.gehring at embl.de
Thu Feb 27 14:05:31 CET 2014
Subestting your vector returns an element with both value and name set
to 'NA'. In contrast, subsetting the 'Seqinfo' object returns an
element with 'seqname' set to the key - which can be easily
misinterpreted.. Also, subsetting a GRanges (e.g. 'as(si, "GRanges")')
with a non-existing key throws an error.
On 27/02/14 14:00, Dan Du wrote:
> To me it sounds like what I am expecting, from a R base point of view.
> On Thu, 2014-02-27 at 13:49 +0100, Julian Gehring wrote:
>> In the current bioc-stable and bioc-devel, a 'Seqinfo' object can be
>> indexed successfully with any character key, even it is non-existing:
>> #+BEGIN_SRC R
>> si = seqinfo(BSgenome.Hsapiens.UCSC.hg19)
>> ind2 = "999"
>> ind2 %in% seqnames(si) ## FALSE, no seqlevel with this name
>> si[ind2] ## works, but should not
>> Shouldn't this throw an error?
>> Best wishes
>> Bioc-devel at r-project.org mailing list
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