BiocGenerics (version 0.18.0)

BiocGenerics-package: 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 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::append

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:

• 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 package parallel:

• BiocGenerics::clusterCall, BiocGenerics::clusterApply, BiocGenerics::clusterApplyLB, BiocGenerics::clusterEvalQ, BiocGenerics::clusterExport, BiocGenerics::clusterMap, BiocGenerics::clusterSplit, BiocGenerics::parLapply, BiocGenerics::parSapply, BiocGenerics::parApply, BiocGenerics::parRapply, BiocGenerics::parCapply, BiocGenerics::parLapplyLB, BiocGenerics::parSapplyLB

(2) Bioconductor specific generics

• annotation, annotation<-

combine

dbconn, dbfile

fileName

normalize

organism, organism<-, species, species<-

plotMA

plotPCA

score, score<-

strand, strand<-, invertStrand

updateObject

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')