Generic functions for Bioconductor

Description

S4 generic functions needed by many other Bioconductor packages.

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

From package base:

• BiocGenerics::cbind, BiocGenerics::rbind

• 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::lapply, BiocGenerics::sapply

• BiocGenerics::mapply

• BiocGenerics::nrow, BiocGenerics::ncol, BiocGenerics::NROW, BiocGenerics::NCOL

• BiocGenerics::order

• BiocGenerics::paste

• BiocGenerics::rep.int

• BiocGenerics::rownames, BiocGenerics::colnames

• sets: BiocGenerics::union, BiocGenerics::intersect, BiocGenerics::setdiff

• BiocGenerics::table

• BiocGenerics::tapply

• BiocGenerics::unique

From package graphics:

• BiocGenerics::boxplot

• BiocGenerics::image

From package stats:

• BiocGenerics::density

• BiocGenerics::residuals

• BiocGenerics::weights

• BiocGenerics::xtabs

(2) Bioconductor specific generics

• combine

• strand, strand<-

• 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.

Author(s)

The Bioconductor Dev Team

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.

Examples

## List all the symbols defined in this package:
ls('package:BiocGenerics')