On 11/06/2013 11:29 AM, Michael Lawrence wrote:
Great, thanks for updating. I legitimately wanted to use %in%, not %over%.
Great to hear you have a use case for %in% (with the new behavior). So I'm not the only one ;-) H.
Michael On Wed, Nov 6, 2013 at 10:59 AM, Hervé Pagès <hpa...@fhcrc.org <mailto:hpa...@fhcrc.org>> wrote: Hi Michael, On 11/05/2013 04:30 PM, Michael Lawrence wrote: I'm getting a little tired of this one popping up: In x %in% other : Starting with BioC 2.12, the behavior of %in% on GenomicRanges objects has changed to use *equality* instead of *overlap* for comparing elements between GenomicRanges objects 'x' and 'table'. Now 'x[i]' and 'table[j]' are considered to match when they are equal (i.e. 'x[i] == table[j]'), instead of when they overlap. This new behavior is consistent with base::`%in%`(). If you need the old behavior, please use: query %over% subject Now that even release is Bioc 2.13, can we remove it? And there might be others. If you use %over% you don't get the warning ;-) Anyway this is gone in BioC 2.14 as part of the normal process of removing features that were defunct in BioC 2.13. Cheers, H. Thanks, 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
