BiocGenerics-package: S4 generic functions for Bioconductor

In Bioconductor/BiocGenerics: S4 generic functions used in Bioconductor

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

• 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')

Bioconductor/BiocGenerics documentation built on Nov. 17, 2024, 6:52 p.m.