BiocGenerics-package {BiocGenerics} | R Documentation |
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.list
-
BiocGenerics::as.vector
-
BiocGenerics::colSums
,BiocGenerics::rowSums
,BiocGenerics::colMeans
,BiocGenerics::rowMeans
-
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::is.unsorted
-
BiocGenerics::mapply
-
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::pos
-
BiocGenerics::subset
-
BiocGenerics::table
-
BiocGenerics::tapply
-
BiocGenerics::unique
-
BiocGenerics::unlist
-
BiocGenerics::unsplit
-
BiocGenerics::which
Generics for functions defined in package utils:
-
BiocGenerics::relist
Generics for functions defined in package graphics:
Generics for functions defined in package stats:
(2) Bioconductor specific generics
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 forBiocGenerics::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
andsetMethod
for defining generics and methods.
Examples
## List all the symbols defined in this package:
ls('package:BiocGenerics')