[Bioc-devel] adding methods to BiocGenerics

[Laurent Gatto]

On 19 May 2017 15:39, Stephanie M. Gogarten wrote:

> Dear Core Team,
>
> What do you think about adding the following generics to BiocGenerics?
>
> colData
> rowRanges
> ref
> alt
> qual

Currently exists in MSnbase with signature

  setGeneric("qual", function(object) standardGeneric("qual"))

As far as I know, only used in that packages. I'm more than happy to use
BiocGenerics::qual when/if it becomes available.

> filt
> header

Currently exists in mzR with signature

  setGeneric("header", function(object, scans, ...) standardGeneric("header"))

and is used at least in mzR and MSnbase.

I guess that signature, as it is, wouldn't be a good for BiocGenerics.

Best wishes,

Laurent

> fixed
> info
> geno
>
> They are currently defined by both 
> VariantAnnotation/SummarizedExperiment and SeqArray. Given the 
> increasingly widespread use of VCF files, it seems likely that other 
> packages may want to use them in future also.
>
> Stephanie
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/