Re: [Bioc-devel] warning when merging disjoint sets of seqlevels
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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] warning when merging disjoint sets of seqlevels
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 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] warning when merging disjoint sets of seqlevels
On 10/13/2014 07:45 AM, Michael Lawrence wrote: 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? What has changed is that now we get the warning for the edge-case where one of the 2 Seqinfo objects is empty. In that particular case the warning is arguably not useful so I just removed it. H. On Sun, Oct 12, 2014 at 11:46 PM, Hervé Pagès hpa...@fhcrc.org mailto: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 mailto:Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/__listinfo/bioc-devel 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 mailto:hpa...@fhcrc.org Phone: (206) 667-5791 tel:%28206%29%20667-5791 Fax: (206) 667-1319 tel:%28206%29%20667-1319 -- 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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] warning when merging disjoint sets of seqlevels
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. Michael [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
