[Bioc-devel] GenomicRanges: Seqinfo indexing with non-existing key
Hi Julian, Ah, yes, the name part could have been improved, maybe something like, Seqinfo of length 1 seqnames seqlengths isCircular genome <NA> NA NA <NA> My thoughts was more on the error part. For those inconsistencies, you may have to wait for some core member to chime-in. Best, Dan
On Thu, 2014-02-27 at 14:05 +0100, Julian Gehring wrote:
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.. 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
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