[Bioc-devel] adding methods to BiocGenerics

Laurent Gatto lg390 at cam.ac.uk
Fri May 19 17:57:25 CEST 2017

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,


> 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
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Laurent Gatto | @lgatt0

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