BiocGenerics-package

S4 generic functions for Bioconductor

S4 generic functions needed by many Bioconductor packages.

Keywords
package
Details

We divide the generic functions defined in the BiocGenerics package in 2 categories: (1) functions already defined in base R and explicitly promoted to generics in BiocGenerics, and (2) Bioconductor specific generics.

(1) Functions defined in base R and explicitly promoted to generics in the BiocGenerics package

Generics for functions defined in package base:

  • BiocGenerics::as.data.frame
  • BiocGenerics::as.vector
  • BiocGenerics::cbind, BiocGenerics::rbind
  • BiocGenerics::do.call
  • BiocGenerics::duplicated, BiocGenerics::anyDuplicated
  • BiocGenerics::eval
  • Extremes: BiocGenerics::pmax, BiocGenerics::pmin, BiocGenerics::pmax.int, BiocGenerics::pmin.int
  • funprog: BiocGenerics::Reduce, BiocGenerics::Filter, BiocGenerics::Find, BiocGenerics::Map, BiocGenerics::Position
  • BiocGenerics::get, BiocGenerics::mget
  • BiocGenerics::grep, BiocGenerics::grepl
  • BiocGenerics::is.unsorted
  • BiocGenerics::lapply, BiocGenerics::sapply
  • BiocGenerics::lengths
  • BiocGenerics::mapply
  • BiocGenerics::match
  • BiocGenerics::nrow, BiocGenerics::ncol, BiocGenerics::NROW, BiocGenerics::NCOL
  • BiocGenerics::order
  • BiocGenerics::paste
  • BiocGenerics::rank
  • BiocGenerics::rep.int
  • BiocGenerics::rownames, BiocGenerics::rownames<-, BiocGenerics::colnames, BiocGenerics::colnames<-
  • sets: BiocGenerics::union, BiocGenerics::intersect, BiocGenerics::setdiff
  • BiocGenerics::sort
  • BiocGenerics::start, BiocGenerics::start<-, BiocGenerics::end, BiocGenerics::end<-, BiocGenerics::width, BiocGenerics::width<-
  • BiocGenerics::subset
  • BiocGenerics::table
  • BiocGenerics::tapply
  • BiocGenerics::unique
  • BiocGenerics::unlist
  • Generics for functions defined in package utils:

    Generics for functions defined in package graphics:

  • BiocGenerics::image
  • Generics for functions defined in package stats:

  • BiocGenerics::residuals
  • BiocGenerics::weights
  • BiocGenerics::xtabs
  • Generics for functions defined in package parallel:

    (2) Bioconductor specific generics

  • combine
  • dbconn, dbfile
  • fileName
  • normalize
  • organism, organism<-, species, species<-
  • plotMA
  • plotPCA
  • score, score<-
  • strand, strand<-, invertStrand
  • updateObject
  • Note

    More generics can be added on request by sending an email to the Bioc-devel mailing list:

    http://bioconductor.org/help/mailing-list/

    Things that should NOT be added to the BiocGenerics package:

    • Internal generic primitive functions like length, dim, `dim<-`, etc... See ?InternalMethods for the complete list. There are a few exceptions though, that is, the BiocGenerics package may actually redefine a few of those internal generic primitive functions as S4 generics when for example the signature of the internal generic primitive is not appropriate (this is the case for BiocGenerics::cbind).

  • S3 and S4 group generic functions like Math, Ops, etc... See ?groupGeneric and ?S4groupGeneric for the complete list.
  • Generics already defined in the stats4 package.
  • See Also

    • showMethods for displaying a summary of the methods defined for a given generic function.

    • selectMethod for getting the definition of a specific method.

    • setGeneric and setMethod for defining generics and methods.

    Aliases
    • BiocGenerics-package
    • BiocGenerics
    Examples
    ## List all the symbols defined in this package:
    ls('package:BiocGenerics')
    
    Documentation reproduced from package BiocGenerics, version 0.18.0, License: Artistic-2.0

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