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 <hpa...@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@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: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel