Re: [Bioc-devel] Listing package-specific methods
There are two relevant queries: 1) What are the methods where at least one signature component is (or extends) this class? 2) What are the methods for this class that are defined in a specific package? #1 is along the lines of what Vince said. I prefer that definition, because I often want to see the methods that are specific to the semantics of the subclass. It does not matter which package implements the methods. I think it could be supported via methods(class="DESeqDataSet", inherit=FALSE). But we might want a more convenient interface. Optionally displaying the signatures would also be good. One of the problems is that methods are not easily accessible objects in the search path like ordinary functions. There is no equivalent of ls(2), and it's tougher to retrieve the definition. Maybe the IDE could help out? For example, when typing the name of a generic, in addition to the prompt with argument names, it could list the methods. Type-ahead could be smart enough to handle method selection. Or, one could enter a symbol like `findOverlaps,Ranges,Ranges` but the search would need to be dynamic to handle method selection. Maybe the generic function could be modeled as a container of its methods? Like findOverlaps$IRanges (second argument wildcard) or findOverlaps$"IRanges,IRanges" to further restrict. Doing the same from the class perspective semantically clashes with S4. I just don't like the IRanges$findOverlaps syntax. It also would require formal treatment of constructors. On Mon, Jun 27, 2016 at 9:39 AM, Michael Love wrote: > hi, > > Following on a conversation from Bioc2016, I think it would be good to have > a function available to Bioconductor users that helps in the following > situation: > > I'm a user, trying out a new package 'foo', which defines the FooData > class, that builds on top of SummarizedExperiment. The package author has > defined a set of methods for the FooData class in the 'foo' package. From > the R console, I want to see a list of these methods, but I don't want to > look through the entire list of methods defined for SummarizedExperiment, > Vector, and Annotated. > > I think such a function should live somewhere easily accessible for > Bioconductor users. I worked out two implementations of this function which > you can see here: > > http://rpubs.com/mikelove/pkgmethods > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Listing package-specific methods
This seems like a pretty simple solution, so I like that :) On Mon, Jun 27, 2016 at 10:46 AM, Hervé Pagès wrote: > Hi Mike, > > IIUC you want to do something like > > setdiff(methods(class="DESeqDataSet"), > methods(class="RangedSummarizedExperiment")) > > Maybe this could be handled by methods() itself e.g. with > an extra argument that lets the user choose if s/he wants to see > all the methods (i.e. specific + inherited) or only the specific > ones? > > H. > > On 06/27/2016 09:39 AM, Michael Love wrote: > >> hi, >> >> Following on a conversation from Bioc2016, I think it would be good to >> have >> a function available to Bioconductor users that helps in the following >> situation: >> >> I'm a user, trying out a new package 'foo', which defines the FooData >> class, that builds on top of SummarizedExperiment. The package author has >> defined a set of methods for the FooData class in the 'foo' package. From >> the R console, I want to see a list of these methods, but I don't want to >> look through the entire list of methods defined for SummarizedExperiment, >> Vector, and Annotated. >> >> I think such a function should live somewhere easily accessible for >> Bioconductor users. I worked out two implementations of this function >> which >> you can see here: >> >> http://rpubs.com/mikelove/pkgmethods >> >> [[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...@fredhutch.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] Listing package-specific methods
Hi Mike, IIUC you want to do something like setdiff(methods(class="DESeqDataSet"), methods(class="RangedSummarizedExperiment")) Maybe this could be handled by methods() itself e.g. with an extra argument that lets the user choose if s/he wants to see all the methods (i.e. specific + inherited) or only the specific ones? H. On 06/27/2016 09:39 AM, Michael Love wrote: hi, Following on a conversation from Bioc2016, I think it would be good to have a function available to Bioconductor users that helps in the following situation: I'm a user, trying out a new package 'foo', which defines the FooData class, that builds on top of SummarizedExperiment. The package author has defined a set of methods for the FooData class in the 'foo' package. From the R console, I want to see a list of these methods, but I don't want to look through the entire list of methods defined for SummarizedExperiment, Vector, and Annotated. I think such a function should live somewhere easily accessible for Bioconductor users. I worked out two implementations of this function which you can see here: http://rpubs.com/mikelove/pkgmethods [[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...@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] Listing package-specific methods
1) I guess if someone else defined methods for the FooData class then those
could be of interest, but I think nearly all of the time I want to know
just what this specific package author has defined.
2) This is getting down to my (perhaps idiosyncratic) wants, but I would
like a quick and short printout to the console, so that I can recall the
names (maybe I just forgot) or to look up the man page. So the signatures
then just take up extra space IMO.
On Mon, Jun 27, 2016 at 10:08 AM, Vincent Carey
wrote:
> 1) is the package connection key, or is it the 'directness' of the method
> in connection
>
> with the class of interest? (sorry to be so vague, there must be a more
> scientific term...)
>
> 2) it seems useful to get the signature too. this uses string operations
> to get at something that
>
> the class system likely "knows about" but seems to get close to your target
>
> > directMethods = function(cl) {
>
> + grep(cl, methods(class=cl), value=TRUE)
>
> + }
>
> > directMethods(class(dds))
>
> [1] "coef.DESeqDataSet"
>
> [2] "coerce,DESeqDataSet,RangedSummarizedExperiment-method"
>
> [3] "coerce<-,DESeqDataSet,RangedSummarizedExperiment-method"
>
> [4] "counts,DESeqDataSet-method"
>
> [5] "counts<-,DESeqDataSet,matrix-method"
>
> [6] "design,DESeqDataSet-method"
>
> [7] "design<-,DESeqDataSet,formula-method"
>
> [8] "dispersionFunction,DESeqDataSet-method"
>
> [9] "dispersionFunction<-,DESeqDataSet,function-method"
>
> [10] "dispersions,DESeqDataSet-method"
>
> [11] "dispersions<-,DESeqDataSet,numeric-method"
>
> [12] "estimateDispersions,DESeqDataSet-method"
>
> [13] "estimateSizeFactors,DESeqDataSet-method"
>
> [14] "normalizationFactors,DESeqDataSet-method"
>
> [15] "normalizationFactors<-,DESeqDataSet,matrix-method"
>
> [16] "plotDispEsts,DESeqDataSet-method"
>
> [17] "plotMA,DESeqDataSet-method"
>
> [18] "sizeFactors,DESeqDataSet-method"
>
> [19] "sizeFactors<-,DESeqDataSet,numeric-method"
>
> On Mon, Jun 27, 2016 at 9:39 AM, Michael Love > wrote:
>
>> hi,
>>
>> Following on a conversation from Bioc2016, I think it would be good to
>> have
>> a function available to Bioconductor users that helps in the following
>> situation:
>>
>> I'm a user, trying out a new package 'foo', which defines the FooData
>> class, that builds on top of SummarizedExperiment. The package author has
>> defined a set of methods for the FooData class in the 'foo' package. From
>> the R console, I want to see a list of these methods, but I don't want to
>> look through the entire list of methods defined for SummarizedExperiment,
>> Vector, and Annotated.
>>
>> I think such a function should live somewhere easily accessible for
>> Bioconductor users. I worked out two implementations of this function
>> which
>> you can see here:
>>
>> http://rpubs.com/mikelove/pkgmethods
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Listing package-specific methods
1) is the package connection key, or is it the 'directness' of the method
in connection
with the class of interest? (sorry to be so vague, there must be a more
scientific term...)
2) it seems useful to get the signature too. this uses string operations
to get at something that
the class system likely "knows about" but seems to get close to your target
> directMethods = function(cl) {
+ grep(cl, methods(class=cl), value=TRUE)
+ }
> directMethods(class(dds))
[1] "coef.DESeqDataSet"
[2] "coerce,DESeqDataSet,RangedSummarizedExperiment-method"
[3] "coerce<-,DESeqDataSet,RangedSummarizedExperiment-method"
[4] "counts,DESeqDataSet-method"
[5] "counts<-,DESeqDataSet,matrix-method"
[6] "design,DESeqDataSet-method"
[7] "design<-,DESeqDataSet,formula-method"
[8] "dispersionFunction,DESeqDataSet-method"
[9] "dispersionFunction<-,DESeqDataSet,function-method"
[10] "dispersions,DESeqDataSet-method"
[11] "dispersions<-,DESeqDataSet,numeric-method"
[12] "estimateDispersions,DESeqDataSet-method"
[13] "estimateSizeFactors,DESeqDataSet-method"
[14] "normalizationFactors,DESeqDataSet-method"
[15] "normalizationFactors<-,DESeqDataSet,matrix-method"
[16] "plotDispEsts,DESeqDataSet-method"
[17] "plotMA,DESeqDataSet-method"
[18] "sizeFactors,DESeqDataSet-method"
[19] "sizeFactors<-,DESeqDataSet,numeric-method"
On Mon, Jun 27, 2016 at 9:39 AM, Michael Love
wrote:
> hi,
>
> Following on a conversation from Bioc2016, I think it would be good to have
> a function available to Bioconductor users that helps in the following
> situation:
>
> I'm a user, trying out a new package 'foo', which defines the FooData
> class, that builds on top of SummarizedExperiment. The package author has
> defined a set of methods for the FooData class in the 'foo' package. From
> the R console, I want to see a list of these methods, but I don't want to
> look through the entire list of methods defined for SummarizedExperiment,
> Vector, and Annotated.
>
> I think such a function should live somewhere easily accessible for
> Bioconductor users. I worked out two implementations of this function which
> you can see here:
>
> http://rpubs.com/mikelove/pkgmethods
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Listing package-specific methods
hi, Following on a conversation from Bioc2016, I think it would be good to have a function available to Bioconductor users that helps in the following situation: I'm a user, trying out a new package 'foo', which defines the FooData class, that builds on top of SummarizedExperiment. The package author has defined a set of methods for the FooData class in the 'foo' package. From the R console, I want to see a list of these methods, but I don't want to look through the entire list of methods defined for SummarizedExperiment, Vector, and Annotated. I think such a function should live somewhere easily accessible for Bioconductor users. I worked out two implementations of this function which you can see here: http://rpubs.com/mikelove/pkgmethods [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] 15th Bioconductor birthday coming up
Hi, I was just digging up some stats on BioC, and I found in the SVN the first commit: r21 | rgentlem | 2001-07-29 23:51:48 +0200 (So, 29 Jul 2001) So we should not forget to celebrate the 15th anniversary in ~4 weeks this year, or put up blog posts somewhere. Other things you can learn from the treasure of SVN is that as of 27.06.2016 we had ~119.000 commits by 865 contributors, so since 100k commits this took us a bit more than a year. https://stat.ethz.ch/pipermail/bioc-devel/2015-February/007024.html If the pace continues, 2016 will see more commits than any previous year! Yours, Steffen P.S.: Annual breakdown of commits into trunk/madman/Rpacks, I didn't look at the other branches which have a smaller, but >0 count of commits 5570 2016 10791 2015 8838 2014 8793 2013 7584 2012 7126 2011 5438 2010 5818 2009 5271 2008 4812 2007 4076 2006 3697 2005 2663 2004 2880 2003 1565 2002 196 2001 -- IPB HalleAG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
