Re: [Bioc-devel] Hunting for the subset generic definition?
Done in BiocGenerics 0.15.4. H. On 07/29/2015 11:00 AM, Hervé Pagès wrote: Hi Steve, On 07/29/2015 10:40 AM, Steve Lianoglou wrote: Hi folks, I'm looking to define a `subset` method on an S4 class of mine, but can't find where to import the generic from. That's because subset() is an implicit generic, that is, there is no setGeneric statement for it, only setMethod statements. And so it's automatically turned into a generic the first time a package with a setMethod statement is loaded. More precisely, everything happens as if setGeneric(subset) was called right before the first time setMethod(subset, ...) is called. I can't seem to find it anywhere in: * BiocGenerics * S4Vectors * XVector ( Even though S4Vectors has a: setMethod(subset, DataTable, ...) It's not clear to me where it pulled the appropriate `setGeneric(subset, ...)` from. I believe that you need to import it from S4Vectors. But things are going to be much clearer/cleaner if we make subset() an explicit generic by adding setGeneric(subset) to BiocGenerics. Which I'm going to do right now. Then you'll be able to import the subset() generic from BiocGenerics. Cheers, H. Can anyone provide a pointer? Thanks, -steve -- 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...@fredhutch.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] Hunting for the subset generic definition?
From base, according to my R console: subset standardGeneric for subset defined from package base function (x, ...) standardGeneric(subset) environment: 0x4eb60c8 Methods may be defined for arguments: x Use showMethods(subset) for currently available ones. On 07/29/2015 10:40 AM, Steve Lianoglou wrote: Hi folks, I'm looking to define a `subset` method on an S4 class of mine, but can't find where to import the generic from. I can't seem to find it anywhere in: * BiocGenerics * S4Vectors * XVector ( Even though S4Vectors has a: setMethod(subset, DataTable, ...) It's not clear to me where it pulled the appropriate `setGeneric(subset, ...)` from. Can anyone provide a pointer? Thanks, -steve ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Hunting for the subset generic definition?
Hi Steve, On 07/29/2015 10:40 AM, Steve Lianoglou wrote: Hi folks, I'm looking to define a `subset` method on an S4 class of mine, but can't find where to import the generic from. That's because subset() is an implicit generic, that is, there is no setGeneric statement for it, only setMethod statements. And so it's automatically turned into a generic the first time a package with a setMethod statement is loaded. More precisely, everything happens as if setGeneric(subset) was called right before the first time setMethod(subset, ...) is called. I can't seem to find it anywhere in: * BiocGenerics * S4Vectors * XVector ( Even though S4Vectors has a: setMethod(subset, DataTable, ...) It's not clear to me where it pulled the appropriate `setGeneric(subset, ...)` from. I believe that you need to import it from S4Vectors. But things are going to be much clearer/cleaner if we make subset() an explicit generic by adding setGeneric(subset) to BiocGenerics. Which I'm going to do right now. Then you'll be able to import the subset() generic from BiocGenerics. Cheers, H. Can anyone provide a pointer? Thanks, -steve -- 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...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
