[Bioc-devel] warning when merging disjoint sets of seqlevels

[Michael Lawrence]

But the behavior has changed for this case:

merge(Seqinfo("chr1"), Seqinfo())

Before it was "each has seqlevels not in the other" but now it is "these
two sets are disjoint". Subtle difference, but I think it's important?


On Sun, Oct 12, 2014 at 11:46 PM, Hervé Pagès <hpages at fhcrc.org> wrote:

> Hi Michael,
>
>
> On 10/12/2014 02:02 PM, Michael Lawrence wrote:
>
>> This recently became a warning, and I am not sure why. Yes, in the overlap
>> case, that might be something to worry about. But a perfectly reasonable
>> use case of merge,Seqinfo is to merge two disjoint sets of seqlevels. Now
>> we're forced to use suppressWarnings() for that.
>>
>
> For that use case, nothing has changed, we've always had a warning and
> we still have it.
>
> With BioC 2.14:
>
>   > merge(Seqinfo("chr1"), Seqinfo("chr2"))
>   Seqinfo of length 2
>   seqnames seqlengths isCircular genome
>   chr1             NA         NA   <NA>
>   chr2             NA         NA   <NA>
>   Warning message:
>   In .Seqinfo.mergexy(x, y) :
>     Each of the 2 combined objects has sequence levels not in the other:
>     - in 'x': chr1
>     - in 'y': chr2
>     Make sure to always combine/compare objects based on the same reference
>     genome (use suppressWarnings() to suppress this warning).
>
> With BioC 3.0:
>
>   > merge(Seqinfo("chr1"), Seqinfo("chr2"))
>   Seqinfo object with 2 sequences from an unspecified genome; no
> seqlengths:
>     seqnames seqlengths isCircular genome
>     chr1             NA         NA   <NA>
>     chr2             NA         NA   <NA>
>   Warning message:
>   In .Seqinfo.mergexy(x, y) :
>     The 2 combined objects have no sequence levels in common. (Use
>     suppressWarnings() to suppress this warning.)
>
> It's just that the warning is different. The intention was to make
> the new warning more to the point.
>
> H.
>
>
>> Michael
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

	[[alternative HTML version deleted]]