[Bioc-devel] Listing package-specific methods

Vincent Carey stvjc at channing.harvard.edu
Mon Jun 27 19:08:15 CEST 2016

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 <michaelisaiahlove at gmail.com>

> 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
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> Bioc-devel at r-project.org mailing list
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