[Bioc-devel] Generic for write to BiocGenerics

[Hervé Pagès]

Hi jo,

At the moment probably not much to be gained unless you ran into
some conflicts with other "write" methods defined in Bioconductor?

Note that the arguments/signature of base::write() don't really
help making it a clean generic functions (e.g. weird 'file' default,
'ncolumns' and 'sep' args that lack generality, no ellipsis). It seems
to me that instead of trying to force write() into a generic, it might
be easier/cleaner to define a method for the export() generic defined
in rtracklayer. Maybe the discussion would be whether we should consider
moving rtracklayer::export() to BiocGenerics?

Finally, IMO there is nothing wrong in using specific write* names like
writeMgfData, writeMSData, writeMzTabData, etc... It plays nicely with
tab-completion, the user can use args() to quickly see all the args and
their defaults, tab-completion also works on the arguments, and the user
does not struggle in finding the man page (like s/he does sometimes
with generic and methods, especially when those are defined in
different packages).

H.


On 09/18/2017 10:21 AM, Rainer Johannes wrote:
> Dear all!
>
> We are currently implementing mzML write support in `MSnbase` and did
> implement a `write` method for the S4 objects in `MSnbase`. Now, the
> question is whether it might not be better to define a `write` S4
> generic in `BiocGenerics`?
>
>
> cheers, jo
>
>
>
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-- 
Hervé Pagès

Program in Computational Biology
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