BiocGenerics-package {BiocGenerics} | R Documentation |
S4 generic functions needed by many Bioconductor packages.
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.
Generics for functions defined in package base:
BiocGenerics::as.data.frame
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::mapply
BiocGenerics::match
BiocGenerics::nrow
,
BiocGenerics::ncol
,
BiocGenerics::NROW
,
BiocGenerics::NCOL
BiocGenerics::order
BiocGenerics::paste
BiocGenerics::rank
BiocGenerics::rep.int
sets:
BiocGenerics::union
,
BiocGenerics::intersect
,
BiocGenerics::setdiff
BiocGenerics::sort
BiocGenerics::table
BiocGenerics::tapply
BiocGenerics::unique
BiocGenerics::unlist
Generics for functions defined in package graphics:
Generics for functions defined in package stats:
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
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.
The Bioconductor Dev Team
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.
## List all the symbols defined in this package: ls('package:BiocGenerics')