[Bioc-devel] Listing package-specific methods

[Michael Love]

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 <stvjc at channing.harvard.edu>
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 <michaelisaiahlove at gmail.com
> > 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
>>
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>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>

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