[Bioc-devel] Generic for write to BiocGenerics

Rainer Johannes Johannes.Rainer at eurac.edu
Tue Sep 19 08:07:29 CEST 2017

Thanks for the suggestions!

Yes, writeMSData was my first go - but we have already a writeMSData
function in mzR. I didn't want to make that a generic and implement it
for the MS data objects in MSnbase, because I thought that calling a
method `writeMSData,MSnExp` on an object the user knows to contain MS
data might be too much (i.e. it would translate to "write the MS data
from the MS data containing object to a file" while e.g. `write,MSnExp`
would translate to "write the MS data containing object to a file"). I
know is not the best reason for not using writeMSData -

Using export might be a good alternative - does also not interfere with
the base::write. Would be nice if you could add that to BiocGenerics.

thanks, jo

On 09/19/2017 12:22 AM, Michael Lawrence wrote:
> I was also about to suggest that we converge on export() but held back
> because I was obviously biased. I also agree with making the target
> explicit in the function name. It makes the intent of the code way
> more obvious.
> On Mon, Sep 18, 2017 at 3:15 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
>> 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
>>> _______________________________________________
>>> 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
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