[Bioc-devel] Generic for write to BiocGenerics

Hervé Pagès hpages at fredhutch.org
Tue Sep 19 00:15:13 CEST 2017

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).


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
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=10yPFYogq10f-iQf5EwJPYNuEYfi2q0m-34r6ELrqqQ&s=Ukn5OXjj6C3HDU7w5fAKxAeEAhG_9IC3llSKwkgMHCA&e=

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

More information about the Bioc-devel mailing list