S4 generic functions for Bioconductor

Description

S4 generic functions needed by many Bioconductor packages.

Details

We divide the generic functions defined in the BiocGenerics package in 2 categories:

1. Functions already defined in base R or in CRAN package generics, and explicitly promoted to S4 generics in BiocGenerics

2. S4 generics specific to Bioconductor.

(1) Functions defined in base R or CRAN package generics and explicitly promoted to S4 generics in the BiocGenerics package

Generics for functions defined in package base:

• BiocGenerics::aperm

• BiocGenerics::append

• BiocGenerics::as.data.frame

• BiocGenerics::as.list

• BiocGenerics::as.vector

• BiocGenerics::rbind, BiocGenerics::cbind

• BiocGenerics::do.call

• BiocGenerics::duplicated, BiocGenerics::anyDuplicated

• BiocGenerics::eval

• Extremes: BiocGenerics::pmax, BiocGenerics::pmin, BiocGenerics::pmax.int, BiocGenerics::pmin.int

• BiocGenerics::format

• 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::mapply

• BiocGenerics::match, BiocGenerics::%in%

• 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<-

• BiocGenerics::saveRDS

• BiocGenerics::sort

• BiocGenerics::start, BiocGenerics::start<-, BiocGenerics::end, BiocGenerics::end<-, BiocGenerics::width, BiocGenerics::width<-, BiocGenerics::pos

• BiocGenerics::subset

• BiocGenerics::t

• BiocGenerics::table

• BiocGenerics::tapply

• BiocGenerics::unique

• BiocGenerics::unlist

• BiocGenerics::unsplit

• BiocGenerics::which

• BiocGenerics::which.min, BiocGenerics::which.max

Generics for functions defined in package utils:

• BiocGenerics::relist

Generics for functions defined in package graphics:

• BiocGenerics::boxplot

• BiocGenerics::image

Generics for functions defined in package stats:

• BiocGenerics::density

• BiocGenerics::residuals

• BiocGenerics::weights

• BiocGenerics::xtabs

Generics for functions defined in CRAN package generics:

• setops: BiocGenerics::union, BiocGenerics::intersect, BiocGenerics::setdiff, BiocGenerics::setequal

(2) S4 generics specific to Bioconductor

• annotation, annotation<-

• combine

• containsOutOfMemoryData

• dbconn, dbfile

• counts, counts<-, design, design<-, dispTable, dispTable<-, sizeFactors, sizeFactors<-, conditions, conditions<-, estimateSizeFactors, estimateDispersions, plotDispEsts

• dims, nrows, ncols,

• fileName

• longForm

• normalize

• Ontology

• organism, organism<-, species, species<-

• paste2

• path, path<-, basename, basename<-, dirname, dirname<-

• plotMA

• plotPCA

• score, score<-

• strand, strand<-, invertStrand

• toTable

• type, type<-

• 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')