It sounds like everything is working, apart from roxygen 2. This is the
right way to do this; there are many examples; for example findOverlaps for
GenomicRanges, GenomicRanges which support ignore.strand which is not an
argument to the generic; see below. You may have to discuss this with the
roxygen developers; I don't use that framework. But your general idea is
sound.
Best,
Kasper
> findOverlaps
standardGeneric for "findOverlaps" defined from package "IRanges"
function (query, subject, maxgap = 0L, minoverlap = 1L, type = c("any",
"start", "end", "within", "equal"), select = c("all", "first",
"last", "arbitrary"), algorithm = c("nclist", "intervaltree"),
...)
standardGeneric("findOverlaps")
<environment: 0x7fb7815a8518>
Methods may be defined for arguments: query, subject
Use showMethods("findOverlaps") for currently available ones.
> getMethod("findOverlaps", signature("GenomicRanges", "GenomicRanges"))
Method Definition:
function (query, subject, maxgap = 0L, minoverlap = 1L, type = c("any",
"start", "end", "within", "equal"), select = c("all", "first",
"last", "arbitrary"), algorithm = c("nclist", "intervaltree"),
...)
{
.local <- function (query, subject, maxgap = 0L, minoverlap = 1L,
type = c("any", "start", "end", "within", "equal"), select =
c("all",
"first", "last", "arbitrary"), algorithm = c("nclist",
"intervaltree"), ignore.strand = FALSE)
{
type <- match.arg(type)
select <- match.arg(select)
algorithm <- match.arg(algorithm)
if (algorithm == "nclist")
FUN <- findOverlaps_GenomicRanges
else FUN <- findOverlaps_GenomicRanges_old
FUN(query, subject, maxgap = maxgap, minoverlap = minoverlap,
type = type, select = select, ignore.strand = ignore.strand)
}
.local(query, subject, maxgap, minoverlap, type, select,
algorithm, ...)
}
<environment: namespace:GenomicRanges>
Signatures:
query subject
target "GenomicRanges" "GenomicRanges"
defined "GenomicRanges" "GenomicRanges"
On Sun, Sep 20, 2015 at 1:23 PM, Christian Arnold <christian.arn...@embl.de>
wrote:
> Hi all,
>
> I am currently producing the documentation for a new hopefully
> soon-to-be-submitted Bioconductor package and I am facing some difficulties
> with R CMD check.
> In summary: I want to dispatch the existing generic for "counts" to make
> it usable with my object of type SNPhood as well.
>
> The original prototype from BiocGenerics:
>
> standardGeneric for "counts" defined from package "BiocGenerics"
>
> function (object, ...)
>
>
>
> I am calling, as you can see, an internal function for this. Currently,
> because of its original prototype, I use:
>
> setMethod("counts", "SNPhood", function(object, ...) {.getCounts(object,
> ...)})
>
>
>
> However, in my case, I want to use an extended prototype to specify which
> counts exactly should be extracted.
>
> .getCounts <- function(SNPhood.o, type, readGroup = NULL, dataset = NULL,
> ...)
>
>
>
> Everything works, but I want to document the additional arguments
> properly. However, with roxygen 2, I am not sure how to achieve that
> without producing warnings.
>
> I am using:
>
> #' @usage counts (object, type, readGroup, dataset)
>
> #' @template object
>
> #' @param type bla
>
> #' @template readGroup
>
> #' @template dataset
>
>
> This produces:
>
> * checking for code/documentation mismatches ... WARNING
> Codoc mismatches from documentation object 'counts,SNPhood-method':
> counts
> Code: function(object, ...)
> Docs: function(object, type, readGroup, dataset)
> Argument names in code not in docs:
> ...
> Argument names in docs not in code:
> type readGroup dataset
> Mismatches in argument names:
> Position: 2 Code: ... Docs: type
>
>
>
> So, what is the recommended way here? I could write an own "new" counts
> function, but I thought if a generics already exists, I should use it
> because this is exactly what my function does also...
>
>
> Thanks,
> Christian
>
> --
> —————————————————————————
> Christian Arnold, PhD
> Staff Bioinformatician
>
> SCB Unit - Computational Biology
> Joint appointment Genome Biology
> Joint appointment European Bioinformatics Institute (EMBL-EBI)
>
> European Molecular Biology Laboratory (EMBL)
> Meyerhofstrasse 1; 69117, Heidelberg, Germany
>
> Email: christian.arn...@embl.de
> Phone: +49(0)6221-387-8472
> Web: http://www.zaugg.embl.de/
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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