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 <hpa...@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@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: hpa...@fhcrc.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
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