[Bioc-devel] GenomicRanges: Seqinfo indexing with non-existing key
Hi Dan,
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. Since the other columns ('seqlengths', 'genome',
'circular') are in many cases 'NA' anyway, it becomes hard to catch
this. Also, subsetting a GRanges (e.g. 'as(si, "GRanges")') with a
non-existing key throws an error.
Best wishes
Julian
On 27/02/14 14:00, Dan Du wrote:
Hi, To me it sounds like what I am expecting, from a R base point of view. x<-1:5 names(x)<-letters[1:5] i<-'f' x[i] Best, Dan On Thu, 2014-02-27 at 13:49 +0100, Julian Gehring wrote:
Hi, 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 library(GenomicRanges) library(BSgenome.Hsapiens.UCSC.hg19) si = seqinfo(BSgenome.Hsapiens.UCSC.hg19) ind2 = "999" ind2 %in% seqnames(si) ## FALSE, no seqlevel with this name si[ind2] ## works, but should not #+END_SRC Shouldn't this throw an error? Best wishes Julian
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel