[med-svn] [SCM] r-bioc-biocgenerics.git branch, upstream, updated. upstream/0.6.0
Charles Plessy
plessy at debian.org
Sat Apr 6 05:56:40 UTC 2013
The following commit has been merged in the upstream branch:
commit d2469c778ded49f8e5d9b7f0529c2479c637128f
Author: Charles Plessy <plessy at debian.org>
Date: Sat Apr 6 13:36:03 2013 +0900
Imported Upstream version 0.6.0
diff --git a/DESCRIPTION b/DESCRIPTION
index d31aae3..8e11449 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,21 +1,21 @@
Package: BiocGenerics
Title: Generic functions for Bioconductor
-Description: S4 generic functions needed by many other Bioconductor packages.
-Version: 0.4.0
+Description: S4 generic functions needed by many Bioconductor packages.
+Version: 0.6.0
Author: The Bioconductor Dev Team
Maintainer: Bioconductor Package Maintainer
<maintainer at bioconductor.org>
biocViews: Infrastructure
-Depends: methods, graphics, stats
-Imports: methods, graphics, stats
+Depends: methods, graphics, stats, parallel
+Imports: methods, graphics, stats, parallel
Suggests: Biobase, IRanges, GenomicRanges, AnnotationDbi, oligoClasses,
- oligo, affyPLM, RUnit
+ oligo, affyPLM, flowClust, RUnit
License: Artistic-2.0
-Collate: connection-classes.R boxplot.R cbind.R density.R duplicated.R
- eval.R Extremes.R funprog.R get.R image.R lapply.R mapply.R
- nrow.R order.R paste.R rep.R residuals.R row_colnames.R sets.R
- table.R tapply.R unique.R weights.R xtabs.R annotation.R
- combine.R strand.R updateObject.R testPackage.R
- test_BiocGenerics_package.R zzz.R
-Packaged: 2012-10-02 05:09:36 UTC; biocbuild
-InstallableEverywhere: yes
+Collate: S3-classes-as-S4-classes.R as.data.frame.R cbind.R
+ duplicated.R eval.R Extremes.R funprog.R get.R lapply.R
+ mapply.R match.R nrow.R order.R paste.R rank.R rep.R
+ row_colnames.R sets.R sort.R table.R tapply.R unique.R unlist.R
+ boxplot.R image.R density.R residuals.R weights.R xtabs.R
+ clusterApply.R annotation.R combine.R strand.R updateObject.R
+ testPackage.R test_BiocGenerics_package.R zzz.R
+Packaged: 2013-04-04 08:27:12 UTC; biocbuild
diff --git a/NAMESPACE b/NAMESPACE
index 08de67d..4cb486b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,11 +1,17 @@
import(methods)
import(graphics)
import(stats)
+import(parallel)
exportClasses(
- ## from R/connection-classes.R:
- connection, file, url, gzfile, bzfile, unz, pipe, sockconn,
- terminal, textConnection, gzcon, characterORconnection
+ ## from R/S3-classes-as-S4-classes.R:
+ connection,
+ file, url, gzfile, bzfile, unz, pipe,
+ fifo, sockconn, terminal, textConnection,
+ gzcon,
+ characterORconnection,
+ AsIs
+ #table, xtabs
)
@@ -14,16 +20,14 @@ exportClasses(
### BiocGenerics package
### --------------------------------------------------------------------------
+### Generics for functions defined in package base:
export(
- ## from R/boxplot.R:
- boxplot,
+ ## from R/as.data.frame.R:
+ as.data.frame,
## from R/cbind.R:
cbind, rbind,
- ## from R/density.R:
- density,
-
## from R/duplicated.R:
duplicated, anyDuplicated,
@@ -39,15 +43,15 @@ export(
## from R/get.R:
get, mget,
- ## from R/image.R:
- image,
-
## from R/lapply.R:
lapply, sapply,
## from R/mapply.R:
mapply,
+ ## from R/match.R:
+ match,
+
## from R/nrow.R:
nrow, ncol, NROW, NCOL,
@@ -57,18 +61,21 @@ export(
## from R/paste.R:
paste,
+ ## from R/rank.R:
+ rank,
+
## from R/rep.R:
rep.int,
- ## from R/residuals.R:
- residuals,
-
## from R/row_colnames.R:
rownames, colnames,
## from R/sets.R:
union, intersect, setdiff,
+ ## from R/sort.R:
+ sort,
+
## from R/table.R:
table,
@@ -78,6 +85,27 @@ export(
## from R/unique.R:
unique,
+ ## from R/unlist.R:
+ unlist
+)
+
+### Generics for functions defined in package graphics:
+export(
+ ## from R/boxplot.R:
+ boxplot,
+
+ ## from R/image.R:
+ image
+)
+
+### Generics for functions defined in package stats:
+export(
+ ## from R/density.R:
+ density,
+
+ ## from R/residuals.R:
+ residuals,
+
## from R/weights.R:
weights,
@@ -85,6 +113,16 @@ export(
xtabs
)
+### Generics for functions defined in package parallel:
+export(
+ ## from R/clusterApply.R:
+ clusterCall, clusterApply, clusterApplyLB,
+ clusterEvalQ, clusterExport,
+ clusterMap, clusterSplit,
+ parLapply, parSapply, parApply, parRapply, parCapply,
+ parLapplyLB, parSapplyLB
+)
+
### ==========================================================================
### Bioconductor specific generics and their methods
diff --git a/R/S3-classes-as-S4-classes.R b/R/S3-classes-as-S4-classes.R
new file mode 100644
index 0000000..ea1a60b
--- /dev/null
+++ b/R/S3-classes-as-S4-classes.R
@@ -0,0 +1,26 @@
+### =========================================================================
+### S3 classes as S4 classes
+### -------------------------------------------------------------------------
+###
+### We register some old-style (aka S3) classes as formally defined (aka S4)
+### classes. This allows S4 methods defined in Bioconductor packages to use
+### them in their signatures. Note that dispatch still works without this
+### registration but causes 'R CMD INSTALL' to (gently) complain.
+
+### connection class and subclasses
+.connectionClasses <- c("file", "url", "gzfile", "bzfile", "unz", "pipe",
+ "fifo", "sockconn", "terminal", "textConnection",
+ "gzcon")
+apply(cbind(.connectionClasses, "connection"), 1, setOldClass,
+ where = environment())
+
+setClassUnion("characterORconnection", c("character", "connection"))
+
+### others
+setOldClass("AsIs")
+
+#setOldClass("xtabs", "table") # this seems to cause problems when installing
+ # IRanges:
+ # Warning: replacing previous import
+ # ‘.__C__table’ when loading ‘BiocGenerics’
+
diff --git a/R/image.R b/R/as.data.frame.R
similarity index 53%
copy from R/image.R
copy to R/as.data.frame.R
index 843d3a7..f906d12 100644
--- a/R/image.R
+++ b/R/as.data.frame.R
@@ -1,9 +1,8 @@
### =========================================================================
-### The image() generic
+### The as.data.frame() generic
### -------------------------------------------------------------------------
+###
+### base::as.data.frame is an S3 generic.
-### The corresponding function is an S3 generic function defined in the
-### graphics package.
-
-setGeneric("image")
+setGeneric("as.data.frame", signature="x")
diff --git a/R/boxplot.R b/R/boxplot.R
index 8db447c..378d98e 100644
--- a/R/boxplot.R
+++ b/R/boxplot.R
@@ -1,9 +1,8 @@
### =========================================================================
### The boxplot() generic
### -------------------------------------------------------------------------
-
-### The corresponding function is an S3 generic function defined in the
-### graphics package.
+###
+### graphics::boxplot is an S3 generic.
setGeneric("boxplot")
diff --git a/R/clusterApply.R b/R/clusterApply.R
new file mode 100644
index 0000000..2f17ede
--- /dev/null
+++ b/R/clusterApply.R
@@ -0,0 +1,35 @@
+### =========================================================================
+### The clusterApply() and related generics
+### -------------------------------------------------------------------------
+
+### The corresponding functions are ordinary functions defined in the
+### parallel package.
+
+setGeneric("clusterCall", signature="cl")
+
+setGeneric("clusterApply", signature=c("cl", "x"))
+
+setGeneric("clusterApplyLB", signature=c("cl", "x"))
+
+setGeneric("clusterEvalQ", signature="cl")
+
+setGeneric("clusterExport", signature="cl")
+
+setGeneric("clusterMap", signature="cl")
+
+setGeneric("clusterSplit") # dispatch on all arguments ('cl' and 'seq')
+
+setGeneric("parLapply", signature=c("cl", "X"))
+
+setGeneric("parSapply", signature=c("cl", "X"))
+
+setGeneric("parApply", signature=c("cl", "X"))
+
+setGeneric("parRapply", signature=c("cl", "x"))
+
+setGeneric("parCapply", signature=c("cl", "x"))
+
+setGeneric("parLapplyLB", signature=c("cl", "X"))
+
+setGeneric("parSapplyLB", signature=c("cl", "X"))
+
diff --git a/R/connection-classes.R b/R/connection-classes.R
deleted file mode 100644
index 2c4eaba..0000000
--- a/R/connection-classes.R
+++ /dev/null
@@ -1,12 +0,0 @@
-### =========================================================================
-### Connections as S4 classes
-### -------------------------------------------------------------------------
-###
-
-.connectionClasses <- c("file", "url", "gzfile", "bzfile", "unz", "pipe",
- "fifo", "sockconn", "terminal", "textConnection",
- "gzcon")
-apply(cbind(.connectionClasses, "connection"), 1, setOldClass,
- where = environment())
-
-setClassUnion("characterORconnection", c("character", "connection"))
diff --git a/R/density.R b/R/density.R
index 1a13ddc..14efc36 100644
--- a/R/density.R
+++ b/R/density.R
@@ -1,9 +1,8 @@
### =========================================================================
### The density() generic
### -------------------------------------------------------------------------
-
-### The corresponding function is an S3 generic function defined in the
-### stats package.
+###
+### stats::density is an S3 generic.
setGeneric("density")
diff --git a/R/image.R b/R/image.R
index 843d3a7..32ed970 100644
--- a/R/image.R
+++ b/R/image.R
@@ -1,9 +1,8 @@
### =========================================================================
### The image() generic
### -------------------------------------------------------------------------
-
-### The corresponding function is an S3 generic function defined in the
-### graphics package.
+###
+### graphics::image is an S3 generic.
setGeneric("image")
diff --git a/R/match.R b/R/match.R
new file mode 100644
index 0000000..5bb14a3
--- /dev/null
+++ b/R/match.R
@@ -0,0 +1,18 @@
+### =========================================================================
+### The match() generic
+### -------------------------------------------------------------------------
+###
+### base::match() doesn't have the ... argument. We add it to the generic
+### function defined here. We also set dispatch on the first two args (the
+### 'x' and 'table' args) only!
+
+.match.useAsDefault <-
+ function(x, table, nomatch=NA_integer_, incomparables=NULL, ...)
+ base::match(x, table, nomatch=nomatch, incomparables=incomparables, ...)
+
+setGeneric("match", signature=c("x", "table"),
+ function(x, table, nomatch=NA_integer_, incomparables=NULL, ...)
+ standardGeneric("match"),
+ useAsDefault=.match.useAsDefault
+)
+
diff --git a/R/image.R b/R/rank.R
similarity index 53%
copy from R/image.R
copy to R/rank.R
index 843d3a7..4954af8 100644
--- a/R/image.R
+++ b/R/rank.R
@@ -1,9 +1,7 @@
### =========================================================================
-### The image() generic
+### The rank() generic
### -------------------------------------------------------------------------
+###
-### The corresponding function is an S3 generic function defined in the
-### graphics package.
-
-setGeneric("image")
+setGeneric("rank", signature="x")
diff --git a/R/rep.R b/R/rep.R
index 85ccc8d..fd71dec 100644
--- a/R/rep.R
+++ b/R/rep.R
@@ -19,8 +19,7 @@
### A more natural (and cleaner) thing to do for this generic would be to
### use the same arguments as base::rep.int() (i.e. 'x', 'times') but then
### 'R CMD check' would get confused and think that we are trying to define
-### an S3 method for base::rep() and would complain (observed with R <=
-### 2.12):
+### an S3 method for base::rep and would complain (observed with R <= 2.12):
###
### * checking S3 generic/method consistency ... WARNING
### rep:
@@ -29,9 +28,12 @@
### function(x, times)
###
### so we use the arguments of base::rep() (i.e. 'x', '...') just to make
-### 'R CMD check' happy :-) ... Kind of an ugly hack though :-(
+### 'R CMD check' happy :-) ... Kind of an ugly/silly hack though :-(
+
+.rep.int.useAsDefault <- function(x, ...) base::rep.int(x, ...)
+
setGeneric("rep.int",
function(x, ...) standardGeneric("rep.int"),
- useAsDefault = function(x, ...) base::rep.int(x, ...)
+ useAsDefault=.rep.int.useAsDefault
)
diff --git a/R/residuals.R b/R/residuals.R
index d4f271a..71e2e8a 100644
--- a/R/residuals.R
+++ b/R/residuals.R
@@ -1,9 +1,8 @@
### =========================================================================
### The residuals() generic
### -------------------------------------------------------------------------
-
-### The corresponding function is an S3 generic function defined in the
-### stats package.
+###
+### stats::residuals is an S3 generic.
setGeneric("residuals")
diff --git a/R/image.R b/R/sort.R
similarity index 53%
copy from R/image.R
copy to R/sort.R
index 843d3a7..9252b88 100644
--- a/R/image.R
+++ b/R/sort.R
@@ -1,9 +1,8 @@
### =========================================================================
-### The image() generic
+### The sort() generic
### -------------------------------------------------------------------------
+###
+### base::sort is an S3 generic.
-### The corresponding function is an S3 generic function defined in the
-### graphics package.
-
-setGeneric("image")
+setGeneric("sort", signature="x")
diff --git a/R/table.R b/R/table.R
index 97822ae..db8c747 100644
--- a/R/table.R
+++ b/R/table.R
@@ -17,8 +17,11 @@
#)
### So we use this instead.
+
+.table.useAsDefault <- function(...) base::table(...)
+
setGeneric("table", signature="...",
function(...) standardGeneric("table"),
- useAsDefault = function(...) base::table(...)
+ useAsDefault=.table.useAsDefault
)
diff --git a/R/image.R b/R/unlist.R
similarity index 53%
copy from R/image.R
copy to R/unlist.R
index 843d3a7..3b78ed6 100644
--- a/R/image.R
+++ b/R/unlist.R
@@ -1,9 +1,8 @@
### =========================================================================
-### The image() generic
+### The unlist() generic
### -------------------------------------------------------------------------
+###
+### base::unlist is an S3 generic.
-### The corresponding function is an S3 generic function defined in the
-### graphics package.
-
-setGeneric("image")
+setGeneric("unlist", signature="x")
diff --git a/R/updateObject.R b/R/updateObject.R
index 2cd8c23..9e36f64 100644
--- a/R/updateObject.R
+++ b/R/updateObject.R
@@ -160,7 +160,7 @@ setMethod("updateObject", "environment",
warning("updateObject modifying environment")
}
env <- if (envLocked) new.env() else object
- lapply(ls(object, all=TRUE),
+ lapply(ls(object, all.names=TRUE),
function(elt) { # side-effect!
bindingLocked <- bindingIsLocked(elt, object)
if (!envLocked && bindingLocked)
diff --git a/R/weights.R b/R/weights.R
index d683064..c075a73 100644
--- a/R/weights.R
+++ b/R/weights.R
@@ -1,9 +1,8 @@
### =========================================================================
### The weights() generic
### -------------------------------------------------------------------------
-
-### The corresponding function is an S3 generic function defined in the
-### stats package.
+###
+### stats::weights is an S3 generic.
setGeneric("weights")
diff --git a/TODO b/TODO
index dc0c6c1..681baf0 100644
--- a/TODO
+++ b/TODO
@@ -3,16 +3,8 @@ o Functions defined in base R that would need to be explicitly promoted
made generics by the IRanges package):
From package base:
- - as.data.frame(): implicit generic dispatches on (x, row.names, optional).
- Explicit generic should dispatch on (x) only.
- append(): implicit generic dispatches on (x, values, after).
Explicit generic should dispatch on (x, values) only (or maybe just x?)
- - unlist(): implicit generic dispatches on (x, recursive, use.names).
- Explicit generic should dispatch on (x) only.
- - sort(): implicit generic dispatches on (x, decreasing).
- Explicit generic should dispatch on (x) only.
- - rank(): implicit generic dispatches on (x, na.last, ties.method).
- Explicit generic should dispatch on (x) only.
- as.vector(): implicit generic dispatches on (x, mode).
Explicit generic should dispatch on (x) only.
- is.unsorted(): implicit generic dispatches on (x, na.rm, strictly).
@@ -34,6 +26,8 @@ o Functions defined in base R that would need to be explicitly promoted
- sub(), gsub(): implicit generics dispatch on (pattern, replacement, x,
ignore.case, perl, fixed, useBytes). Explicit generics should dispatch
on (x) only.
+ - range():
+ - by():
From package stats:
- var(): implicit generic dispatches on (x, y, na.rm, use).
diff --git a/man/BiocGenerics-package.Rd b/man/BiocGenerics-package.Rd
index 0c17095..ea9f8b2 100644
--- a/man/BiocGenerics-package.Rd
+++ b/man/BiocGenerics-package.Rd
@@ -7,7 +7,7 @@
\title{Generic functions for Bioconductor}
\description{
- S4 generic functions needed by many other Bioconductor packages.
+ S4 generic functions needed by many Bioconductor packages.
}
\details{
@@ -19,8 +19,10 @@
\subsection{(1) Functions defined in base R and explicitly promoted to
generics in the BiocGenerics package}{
- From package base:
+ Generics for functions defined in package base:
\itemize{
+ \item \code{BiocGenerics::\link[BiocGenerics]{as.data.frame}}
+
\item \code{BiocGenerics::\link[BiocGenerics]{cbind}},
\code{BiocGenerics::\link[BiocGenerics]{rbind}}
@@ -50,6 +52,8 @@
\item \code{BiocGenerics::\link[BiocGenerics]{mapply}}
+ \item \code{BiocGenerics::\link[BiocGenerics]{match}}
+
\item \code{BiocGenerics::\link[BiocGenerics]{nrow}},
\code{BiocGenerics::\link[BiocGenerics]{ncol}},
\code{BiocGenerics::\link[BiocGenerics]{NROW}},
@@ -59,6 +63,8 @@
\item \code{BiocGenerics::\link[BiocGenerics]{paste}}
+ \item \code{BiocGenerics::\link[BiocGenerics]{rank}}
+
\item \code{BiocGenerics::\link[BiocGenerics]{rep.int}}
\item \code{BiocGenerics::\link[BiocGenerics]{rownames}},
@@ -69,21 +75,25 @@
\code{BiocGenerics::\link[BiocGenerics]{intersect}},
\code{BiocGenerics::\link[BiocGenerics]{setdiff}}
+ \item \code{BiocGenerics::\link[BiocGenerics]{sort}}
+
\item \code{BiocGenerics::\link[BiocGenerics]{table}}
\item \code{BiocGenerics::\link[BiocGenerics]{tapply}}
\item \code{BiocGenerics::\link[BiocGenerics]{unique}}
+
+ \item \code{BiocGenerics::\link[BiocGenerics]{unlist}}
}
- From package graphics:
+ Generics for functions defined in package graphics:
\itemize{
\item \code{BiocGenerics::\link[BiocGenerics]{boxplot}}
\item \code{BiocGenerics::\link[BiocGenerics]{image}}
}
- From package stats:
+ Generics for functions defined in package stats:
\itemize{
\item \code{BiocGenerics::\link[BiocGenerics]{density}}
@@ -93,6 +103,24 @@
\item \code{BiocGenerics::\link[BiocGenerics]{xtabs}}
}
+
+ Generics for functions defined in package parallel:
+ \itemize{
+ \item \code{BiocGenerics::\link[BiocGenerics]{clusterCall}},
+ \code{BiocGenerics::\link[BiocGenerics]{clusterApply}},
+ \code{BiocGenerics::\link[BiocGenerics]{clusterApplyLB}},
+ \code{BiocGenerics::\link[BiocGenerics]{clusterEvalQ}},
+ \code{BiocGenerics::\link[BiocGenerics]{clusterExport}},
+ \code{BiocGenerics::\link[BiocGenerics]{clusterMap}},
+ \code{BiocGenerics::\link[BiocGenerics]{clusterSplit}},
+ \code{BiocGenerics::\link[BiocGenerics]{parLapply}},
+ \code{BiocGenerics::\link[BiocGenerics]{parSapply}},
+ \code{BiocGenerics::\link[BiocGenerics]{parApply}},
+ \code{BiocGenerics::\link[BiocGenerics]{parRapply}},
+ \code{BiocGenerics::\link[BiocGenerics]{parCapply}},
+ \code{BiocGenerics::\link[BiocGenerics]{parLapplyLB}},
+ \code{BiocGenerics::\link[BiocGenerics]{parSapplyLB}}
+ }
}
\subsection{(2) Bioconductor specific generics}{
diff --git a/man/Extremes.Rd b/man/Extremes.Rd
index 00fbdd4..cfae8b4 100644
--- a/man/Extremes.Rd
+++ b/man/Extremes.Rd
@@ -13,7 +13,7 @@
parallel maxima and minima of the input values.
NOTE: This man page is for the \code{pmax}, \code{pmin}, \code{pmax.int}
- and \code{pmin.int} S4 generic functions defined in the BiocGenerics
+ and \code{pmin.int} \emph{S4 generic functions} defined in the BiocGenerics
package.
See \code{?base::\link[base]{pmax}} for the default methods
(defined in the base package).
@@ -44,7 +44,7 @@ pmin.int(..., na.rm=FALSE)
See \code{?base::\link[base]{pmax}} for the value returned by the
default methods.
- Specific methods defined in other Bioconductor packages will typically
+ Specific methods defined in Bioconductor packages will typically
return an object of the same class as the input objects.
}
@@ -59,7 +59,8 @@ pmin.int(..., na.rm=FALSE)
a specific method.
\link[IRanges]{pmax,Rle-method} in the IRanges package
- for the \code{pmax} method defined for \link[IRanges]{Rle} objects.
+ for an example of a specific \code{pmax} method (defined for
+ \link[IRanges]{Rle} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/S3-classes-as-S4-classes.Rd b/man/S3-classes-as-S4-classes.Rd
new file mode 100644
index 0000000..f2ab1fc
--- /dev/null
+++ b/man/S3-classes-as-S4-classes.Rd
@@ -0,0 +1,51 @@
+\name{S3-classes-as-S4-classes}
+
+\alias{S3-classes-as-S4-classes}
+
+\alias{connection-class}
+\alias{file-class}
+\alias{url-class}
+\alias{gzfile-class}
+\alias{bzfile-class}
+\alias{unz-class}
+\alias{pipe-class}
+\alias{fifo-class}
+\alias{sockconn-class}
+\alias{terminal-class}
+\alias{textConnection-class}
+\alias{gzcon-class}
+\alias{characterORconnection-class}
+
+\alias{AsIs-class}
+%\alias{table-class}
+%\alias{xtabs-class}
+
+
+\title{S3 classes as S4 classes}
+
+\description{
+ Some old-style (aka S3) classes are turned into formally defined (aka S4)
+ classes by the BiocGenerics package. This allows S4 methods defined in
+ Bioconductor packages to use them in their signatures.
+}
+
+\details{
+ S3 classes currently turned into S4 classes:
+ \itemize{
+ \item connection class and subclasses:
+ connection,
+ file, url, gzfile, bzfile, unz, pipe,
+ fifo, sockconn, terminal, textConnection,
+ gzcon.
+ Addtitionally the characterORconnection S4 class is defined as
+ the union of classes character and connection.
+
+ \item others: AsIs
+ }
+}
+
+\seealso{
+ \link{setOldClass} and \link{setClassUnion} in the methods package.
+}
+
+\keyword{classes}
diff --git a/man/annotation.Rd b/man/annotation.Rd
index fc5ba53..2b6d038 100644
--- a/man/annotation.Rd
+++ b/man/annotation.Rd
@@ -34,8 +34,8 @@ annotation(object, ...) <- value
a specific method.
\link[Biobase]{annotation,eSet-method} in the Biobase
- package for the method defined for \link[Biobase]{eSet}
- objects.
+ package for an example of a specific \code{annotation} method (defined
+ for \link[Biobase]{eSet} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/as.data.frame.Rd b/man/as.data.frame.Rd
new file mode 100644
index 0000000..109202b
--- /dev/null
+++ b/man/as.data.frame.Rd
@@ -0,0 +1,68 @@
+\name{as.data.frame}
+
+\alias{as.data.frame}
+
+\title{Coerce to a data frame}
+
+\description{
+ Function to coerce to a data frame, if possible.
+
+ NOTE: This man page is for the \code{as.data.frame}
+ \emph{S4 generic function} defined in the BiocGenerics package.
+ See \code{?base::\link[base]{as.data.frame}} for the default method
+ (defined in the base package).
+ Bioconductor packages can define specific methods for objects
+ not supported by the default method.
+}
+
+\usage{
+as.data.frame(x, row.names=NULL, optional=FALSE, ...)
+}
+
+\arguments{
+ \item{x}{
+ Any R object.
+ }
+ \item{row.names, optional, ...}{
+ See \code{?base::\link[base]{as.data.frame}} for a description of
+ these arguments.
+ }
+}
+
+\value{
+ A data frame.
+
+ See \code{?base::\link[base]{as.data.frame}} for the value returned
+ by the default method.
+
+ Specific methods defined in Bioconductor packages should
+ behave as consistently as possible with the default method.
+}
+
+\seealso{
+ \code{base::\link[base]{as.data.frame}} for the default
+ \code{as.data.frame} method.
+
+ \code{\link[methods]{showMethods}} for displaying a summary of the
+ methods defined for a given generic function.
+
+ \code{\link[methods]{selectMethod}} for getting the definition of
+ a specific method.
+
+ \link[IRanges]{as.data.frame,Ranges-method} and
+ \link[IRanges]{as.data.frame,DataFrame-method} in the IRanges package
+ for examples of specific \code{as.data.frame} methods (defined for
+ \link[IRanges]{Ranges} and \link[IRanges]{DataFrame} objects,
+ respectively).
+
+ \link{BiocGenerics} for a summary of all the generics defined
+ in the BiocGenerics package.
+}
+
+\examples{
+as.data.frame # note the dispatch on the 'x' arg only
+showMethods("as.data.frame")
+selectMethod("as.data.frame", "ANY") # the default method
+}
+
+\keyword{methods}
diff --git a/man/boxplot.Rd b/man/boxplot.Rd
index 35a0c8a..aa425d0 100644
--- a/man/boxplot.Rd
+++ b/man/boxplot.Rd
@@ -7,7 +7,7 @@
\description{
Produce box-and-whisker plot(s) of the given (grouped) values.
- NOTE: This man page is for the \code{boxplot} S4 generic function
+ NOTE: This man page is for the \code{boxplot} \emph{S4 generic function}
defined in the BiocGenerics package.
See \code{?graphics::\link[graphics]{boxplot}} for the default method
(defined in the graphics package).
@@ -29,7 +29,7 @@ boxplot(x, ...)
See \code{?graphics::\link[graphics]{boxplot}} for the value returned by the
default method.
- Specific methods defined in other Bioconductor packages should
+ Specific methods defined in Bioconductor packages should
behave as consistently as possible with the default method.
}
@@ -44,7 +44,8 @@ boxplot(x, ...)
a specific method.
\link[oligo]{boxplot,FeatureSet-method} in the oligo package
- for the method defined for \link[oligoClasses]{FeatureSet} objects.
+ for an example of a specific \code{boxplot} method (defined for
+ \link[oligoClasses]{FeatureSet} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/cbind.Rd b/man/cbind.Rd
index ca31b0b..6494c87 100644
--- a/man/cbind.Rd
+++ b/man/cbind.Rd
@@ -10,7 +10,7 @@
and combine them by columns or rows, respectively.
NOTE: This man page is for the \code{cbind} and \code{rbind}
- S4 generic functions defined in the BiocGenerics package.
+ \emph{S4 generic functions} defined in the BiocGenerics package.
See \code{?base::\link[base]{cbind}} for the default methods
(defined in the base package).
Bioconductor packages can define specific methods for objects
@@ -38,7 +38,7 @@ rbind(..., deparse.level=1)
See \code{?base::\link[base]{cbind}} for the value returned by the
default methods.
- Specific methods defined in other Bioconductor packages will typically
+ Specific methods defined in Bioconductor packages will typically
return an object of the same class as the input objects.
}
@@ -53,8 +53,8 @@ rbind(..., deparse.level=1)
a specific method.
\link[IRanges]{cbind,DataFrame-method} in the IRanges package
- for the \code{cbind} method defined for \link[IRanges]{DataFrame}
- objects.
+ for an example of a specific \code{cbind} method (defined for
+ \link[IRanges]{DataFrame} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/clusterApply.Rd b/man/clusterApply.Rd
new file mode 100644
index 0000000..cd97606
--- /dev/null
+++ b/man/clusterApply.Rd
@@ -0,0 +1,159 @@
+\name{clusterApply}
+
+\alias{clusterCall}
+\alias{clusterApply}
+\alias{clusterApplyLB}
+\alias{clusterEvalQ}
+\alias{clusterExport}
+\alias{clusterMap}
+\alias{clusterSplit}
+\alias{parLapply}
+\alias{parSapply}
+\alias{parApply}
+\alias{parRapply}
+\alias{parCapply}
+\alias{parLapplyLB}
+\alias{parSapplyLB}
+
+\title{Apply operations using clusters}
+
+\description{
+ These functions provide several ways to parallelize computations
+ using a cluster.
+
+ NOTE: This man page is for the \code{clusterCall}, \code{clusterApply},
+ \code{clusterApplyLB}, \code{clusterEvalQ}, \code{clusterExport},
+ \code{clusterMap}, \code{clusterSplit}, \code{parLapply}, \code{parSapply},
+ \code{parApply}, \code{parRapply}, \code{parCapply}, \code{parLapplyLB},
+ and \code{parSapplyLB} \emph{S4 generic functions} defined in the
+ BiocGenerics package.
+ See \code{?parallel::\link[parallel]{clusterApply}} for the default
+ methods (defined in the parallel package).
+ Bioconductor packages can define specific methods for cluster-like
+ objects not supported by the default methods.
+}
+
+\usage{
+clusterCall(cl=NULL, fun, ...)
+clusterApply(cl=NULL, x, fun, ...)
+clusterApplyLB(cl=NULL, x, fun, ...)
+clusterEvalQ(cl=NULL, expr)
+clusterExport(cl=NULL, varlist, envir=.GlobalEnv)
+clusterMap(cl=NULL, fun, ..., MoreArgs=NULL, RECYCLE=TRUE,
+ SIMPLIFY=FALSE, USE.NAMES=TRUE,
+ .scheduling=c("static", "dynamic"))
+clusterSplit(cl=NULL, seq)
+
+parLapply(cl=NULL, X, fun, ...)
+parSapply(cl=NULL, X, FUN, ..., simplify=TRUE, USE.NAMES=TRUE)
+parApply(cl=NULL, X, MARGIN, FUN, ...)
+parRapply(cl=NULL, x, FUN, ...)
+parCapply(cl=NULL, x, FUN, ...)
+
+parLapplyLB(cl=NULL, X, fun, ...)
+parSapplyLB(cl=NULL, X, FUN, ..., simplify=TRUE, USE.NAMES=TRUE)
+}
+
+\arguments{
+ \item{cl}{
+ A cluster-like object.
+ }
+ \item{x}{
+ A vector-like object for \code{clusterApply} and \code{clusterApplyLB}.
+ A matrix-like object for \code{parRapply} and \code{parCapply}.
+ }
+ \item{seq}{
+ Vector-like object to split.
+ }
+ \item{X}{
+ A vector-like object for \code{parLapply}, \code{parSapply},
+ \code{parLapplyLB}, and \code{parSapplyLB}.
+ An array-like object for \code{parApply}.
+ }
+ \item{fun, ..., expr, varlist, envir, MoreArgs, RECYCLE,
+ SIMPLIFY, USE.NAMES, .scheduling, FUN, simplify, MARGIN}{
+ See \code{?parallel::\link[parallel]{clusterApply}} for a description of
+ these arguments.
+ }
+}
+
+\value{
+ See \code{?parallel::\link[parallel]{clusterApply}} for the value returned
+ by the default methods.
+
+ Specific methods defined in Bioconductor packages should behave like the
+ default methods.
+}
+
+\seealso{
+ \code{parallel::\link[parallel]{clusterApply}} for the default methods.
+
+ \code{\link[methods]{showMethods}} for displaying a summary of the
+ methods defined for a given generic function.
+
+ \code{\link[methods]{selectMethod}} for getting the definition of
+ a specific method.
+
+ \link{BiocGenerics} for a summary of all the generics defined
+ in the BiocGenerics package.
+}
+
+\examples{
+clusterCall # note the dispatch on the 'cl' arg only
+showMethods("clusterCall")
+selectMethod("clusterCall", "ANY") # the default method
+
+clusterApply # note the dispatch on the 'cl' and 'x' args only
+showMethods("clusterApply")
+selectMethod("clusterApply", c("ANY", "ANY")) # the default method
+
+clusterApplyLB # note the dispatch on the 'cl' and 'x' args only
+showMethods("clusterApplyLB")
+selectMethod("clusterApplyLB", c("ANY", "ANY")) # the default method
+
+clusterEvalQ # note the dispatch on the 'cl' arg only
+showMethods("clusterEvalQ")
+selectMethod("clusterEvalQ", "ANY") # the default method
+
+clusterExport # note the dispatch on the 'cl' arg only
+showMethods("clusterExport")
+selectMethod("clusterExport", "ANY") # the default method
+
+clusterMap # note the dispatch on the 'cl' arg only
+showMethods("clusterMap")
+selectMethod("clusterMap", "ANY") # the default method
+
+clusterSplit
+showMethods("clusterSplit")
+selectMethod("clusterSplit", c("ANY", "ANY")) # the default method
+
+parLapply # note the dispatch on the 'cl' and 'X' args only
+showMethods("parLapply")
+selectMethod("parLapply", c("ANY", "ANY")) # the default method
+
+parSapply # note the dispatch on the 'cl' and 'X' args only
+showMethods("parSapply")
+selectMethod("parSapply", c("ANY", "ANY")) # the default method
+
+parApply # note the dispatch on the 'cl' and 'X' args only
+showMethods("parApply")
+selectMethod("parApply", c("ANY", "ANY")) # the default method
+
+parRapply # note the dispatch on the 'cl' and 'x' args only
+showMethods("parRapply")
+selectMethod("parRapply", c("ANY", "ANY")) # the default method
+
+parCapply # note the dispatch on the 'cl' and 'x' args only
+showMethods("parCapply")
+selectMethod("parCapply", c("ANY", "ANY")) # the default method
+
+parLapplyLB # note the dispatch on the 'cl' and 'X' args only
+showMethods("parLapplyLB")
+selectMethod("parLapplyLB", c("ANY", "ANY")) # the default method
+
+parSapplyLB # note the dispatch on the 'cl' and 'X' args only
+showMethods("parSapplyLB")
+selectMethod("parSapplyLB", c("ANY", "ANY")) # the default method
+}
+
+\keyword{methods}
diff --git a/man/connection-class.Rd b/man/connection-class.Rd
deleted file mode 100644
index 20ea9f4..0000000
--- a/man/connection-class.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-\name{connection-class}
-\alias{connection-class}
-\alias{characterORconnection-class}
-\alias{file-class}
-\alias{gzfile-class}
-\alias{bzfile-class}
-\alias{gzcon-class}
-\alias{pipe-class}
-\alias{sockconn-class}
-\alias{unz-class}
-\alias{url-class}
-\alias{terminal-class}
-\alias{textConnection-class}
-
-\title{S4 connection classes}
-\description{ These are S4 representations of the S3 connection classes
- in R. They exist only to support method dispatch on connection types. }
-
-\keyword{classes}
diff --git a/man/density.Rd b/man/density.Rd
index 6fdc0b8..c9dace8 100644
--- a/man/density.Rd
+++ b/man/density.Rd
@@ -8,7 +8,7 @@
The generic function \code{density} computes kernel density
estimates.
- NOTE: This man page is for the \code{density} S4 generic function
+ NOTE: This man page is for the \code{density} \emph{S4 generic function}
defined in the BiocGenerics package.
See \code{?stats::\link[stats]{density}} for the default method
(defined in the stats package).
@@ -30,7 +30,7 @@ density(x, ...)
See \code{?stats::\link[stats]{density}} for the value returned by the
default method.
- Specific methods defined in other Bioconductor packages should
+ Specific methods defined in Bioconductor packages should
behave as consistently as possible with the default method.
}
@@ -45,7 +45,8 @@ density(x, ...)
a specific method.
\link[flowClust]{density,flowClust-method} in the flowClust package
- for the method defined for \link[flowClust]{flowClust} objects.
+ for an example of a specific \code{density} method (defined for
+ \link[flowClust]{flowClust} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/duplicated.Rd b/man/duplicated.Rd
index 6cfc2f2..e939aba 100644
--- a/man/duplicated.Rd
+++ b/man/duplicated.Rd
@@ -11,7 +11,7 @@
logical vector indicating which elements (rows) are duplicates.
NOTE: This man page is for the \code{duplicated} and \code{anyDuplicated}
- S4 generic functions defined in the BiocGenerics package.
+ \emph{S4 generic functions} defined in the BiocGenerics package.
See \code{?base::\link[base]{duplicated}} for the default methods
(defined in the base package).
Bioconductor packages can define specific methods for objects
@@ -43,7 +43,7 @@ anyDuplicated(x, incomparables=FALSE, ...)
\item \code{nrow(x)} when \code{x} is a data frame.
}
- Specific \code{duplicated} methods defined in other Bioconductor
+ Specific \code{duplicated} methods defined in Bioconductor
packages must also return a logical vector of the same length
as \code{x} when \code{x} is a vector-like object, and a logical
vector with one element for each row when \code{x} is a
@@ -52,7 +52,7 @@ anyDuplicated(x, incomparables=FALSE, ...)
The default \code{anyDuplicated} method (see
\code{?base::\link[base]{duplicated}}) returns a single
non-negative integer and so must the specific \code{anyDuplicated}
- methods defined in other Bioconductor packages.
+ methods defined in Bioconductor packages.
\code{anyDuplicated} should always behave consistently with
\code{duplicated}.
@@ -69,7 +69,8 @@ anyDuplicated(x, incomparables=FALSE, ...)
a specific method.
\link[IRanges]{duplicated,Ranges-method} in the IRanges package
- for the method defined for \link[IRanges]{Ranges} objects.
+ for an example of a specific \code{duplicated} method (defined for
+ \link[IRanges]{Ranges} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/eval.Rd b/man/eval.Rd
index f52d95a..0b1479d 100644
--- a/man/eval.Rd
+++ b/man/eval.Rd
@@ -7,7 +7,7 @@
\description{
\code{eval} evaluates an R expression in a specified environment.
- NOTE: This man page is for the \code{eval} S4 generic function
+ NOTE: This man page is for the \code{eval} \emph{S4 generic function}
defined in the BiocGenerics package.
See \code{?base::\link[base]{eval}} for the default method
(defined in the base package).
@@ -44,7 +44,7 @@ eval(expr, envir=parent.frame(),
See \code{?base::\link[base]{eval}} for the value returned by the
default method.
- Specific methods defined in other Bioconductor packages should
+ Specific methods defined in Bioconductor packages should
behave as consistently as possible with the default method.
}
@@ -58,9 +58,9 @@ eval(expr, envir=parent.frame(),
a specific method.
\link[IRanges]{eval,expression,List-method} in the IRanges
- package for the method defined for when the \code{expr} and \code{envir}
- arguments are \link[base]{expression} and \link[IRanges]{List}
- objects, respectively.
+ package for an example of a specific \code{eval} method (defined
+ for when the \code{expr} and \code{envir} arguments are an
+ \link[base]{expression} and a \link[IRanges]{List} object, respectively).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/funprog.Rd b/man/funprog.Rd
index 0870e17..5413577 100644
--- a/man/funprog.Rd
+++ b/man/funprog.Rd
@@ -21,7 +21,7 @@
list-like or vector-like R objects.
NOTE: This man page is for the \code{Reduce}, \code{Filter},
- \code{Find}, \code{Map} and \code{Position} S4 generic functions
+ \code{Find}, \code{Map} and \code{Position} \emph{S4 generic functions}
defined in the BiocGenerics package.
See \code{?base::\link[base]{Reduce}} for the default methods
(defined in the base package).
@@ -55,8 +55,8 @@ Position(f, x, right=FALSE, nomatch=NA_integer_)
See \code{?base::\link[base]{Reduce}} for the value returned by the
default methods.
- Specific \code{Reduce} methods defined in other Bioconductor packages
- should also return a single integer.
+ Specific methods defined in Bioconductor packages should
+ behave as consistently as possible with the default methods.
}
\seealso{
@@ -70,8 +70,8 @@ Position(f, x, right=FALSE, nomatch=NA_integer_)
a specific method.
\link[IRanges]{Reduce,List-method} in the IRanges package
- for the \code{Reduce} method defined for \link[IRanges]{List}
- objects.
+ for an example of a specific \code{Reduce} method (defined for
+ \link[IRanges]{List} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/get.Rd b/man/get.Rd
index c23ee0c..ffa21cc 100644
--- a/man/get.Rd
+++ b/man/get.Rd
@@ -8,8 +8,8 @@
\description{
Search for an R object with a given name and return it.
- NOTE: This man page is for the \code{get} and \code{mget} S4 generic
- functions defined in the BiocGenerics package.
+ NOTE: This man page is for the \code{get} and \code{mget} \emph{S4 generic
+ functions} defined in the BiocGenerics package.
See \code{?base::\link[base]{get}} for the default methods
(defined in the base package).
Bioconductor packages can define specific methods for objects
@@ -18,11 +18,7 @@
\usage{
get(x, pos=-1, envir=as.environment(pos), mode="any", inherits=TRUE)
-mget(x, envir, mode="any",
- ifnotfound=list(function(x)
- stop(paste0("value for '", x, "' not found"),
- call.=FALSE)),
- inherits=FALSE)
+mget(x, envir, mode="any", ifnotfound, inherits=FALSE)
}
\arguments{
@@ -67,9 +63,9 @@ mget(x, envir, mode="any",
\code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \link[AnnotationDbi]{get,ANY,AnnDbBimap,missing-method} in the
- AnnotationDbi package for the \code{get} method defined for
- \link[AnnotationDbi]{AnnDbBimap} objects.
+ \link[AnnotationDbi]{get,ANY,Bimap,missing-method} in the
+ AnnotationDbi package for an example of a specific \code{get} method
+ (defined for \link[AnnotationDbi]{Bimap} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/image.Rd b/man/image.Rd
index 65c01ea..bd58dac 100644
--- a/man/image.Rd
+++ b/man/image.Rd
@@ -10,7 +10,7 @@
This can be used to display three-dimensional or spatial data aka
\emph{images}.
- NOTE: This man page is for the \code{image} S4 generic function
+ NOTE: This man page is for the \code{image} \emph{S4 generic function}
defined in the BiocGenerics package.
See \code{?graphics::\link[graphics]{image}} for the default method
(defined in the graphics package).
@@ -31,7 +31,7 @@ image(x, ...)
\details{
See \code{?graphics::\link[graphics]{image}} for the details.
- Specific methods defined in other Bioconductor packages should
+ Specific methods defined in Bioconductor packages should
behave as consistently as possible with the default method.
}
@@ -46,7 +46,8 @@ image(x, ...)
a specific method.
\link[oligo]{image,FeatureSet-method} in the oligo package
- for the method defined for \link[oligoClasses]{FeatureSet} objects.
+ for an example of a specific \code{image} method (defined for
+ \link[oligoClasses]{FeatureSet} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/lapply.Rd b/man/lapply.Rd
index b6b08dd..eb2dea4 100644
--- a/man/lapply.Rd
+++ b/man/lapply.Rd
@@ -17,7 +17,7 @@
as \code{lapply(x, f)}.
NOTE: This man page is for the \code{lapply} and \code{sapply}
- S4 generic functions defined in the BiocGenerics package.
+ \emph{S4 generic functions} defined in the BiocGenerics package.
See \code{?base::\link[base]{lapply}} for the default methods
(defined in the base package).
Bioconductor packages can define specific methods for objects
@@ -44,7 +44,7 @@ sapply(X, FUN, ..., simplify=TRUE, USE.NAMES=TRUE)
See \code{?base::\link[base]{lapply}} for the value returned by the
default methods.
- Specific methods defined in other Bioconductor packages should
+ Specific methods defined in Bioconductor packages should
behave as consistently as possible with the default methods.
In particular, \code{lapply} and \code{sapply(simplify=FALSE)}
should always return a list.
@@ -61,8 +61,8 @@ sapply(X, FUN, ..., simplify=TRUE, USE.NAMES=TRUE)
a specific method.
\link[IRanges]{lapply,List-method} in the IRanges package
- for the \code{lapply} method defined for \link[IRanges]{List}
- objects.
+ for an example of a specific \code{lapply} method (defined for
+ \link[IRanges]{List} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/mapply.Rd b/man/mapply.Rd
index 5392747..79098b2 100644
--- a/man/mapply.Rd
+++ b/man/mapply.Rd
@@ -11,7 +11,7 @@
the second elements, the third elements, and so on. Arguments
are recycled if necessary.
- NOTE: This man page is for the \code{mapply} S4 generic function
+ NOTE: This man page is for the \code{mapply} \emph{S4 generic function}
defined in the BiocGenerics package.
See \code{?base::\link[base]{mapply}} for the default method
(defined in the base package).
@@ -39,7 +39,7 @@ mapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE, USE.NAMES=TRUE)
See \code{?base::\link[base]{mapply}} for the value returned by the
default method.
- Specific methods defined in other Bioconductor packages should
+ Specific methods defined in Bioconductor packages should
behave as consistently as possible with the default method.
}
@@ -53,8 +53,8 @@ mapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE, USE.NAMES=TRUE)
a specific method.
\link[IRanges]{mapply,List-method} in the IRanges package
- for the \code{mapply} method defined for \link[IRanges]{List}
- objects.
+ for an example of a specific \code{mapply} method (defined for
+ \link[IRanges]{List} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/match.Rd b/man/match.Rd
new file mode 100644
index 0000000..f96b947
--- /dev/null
+++ b/man/match.Rd
@@ -0,0 +1,77 @@
+\name{match}
+
+\alias{match}
+
+\title{Value matching}
+
+\description{
+ \code{match} returns a vector of the positions of (first) matches of
+ its first argument in its second.
+
+ NOTE: This man page is for the \code{match} \emph{S4 generic function}
+ defined in the BiocGenerics package.
+ See \code{?base::\link[base]{match}} for the default method
+ (defined in the base package).
+ Bioconductor packages can define specific methods for objects
+ (typically vector-like) not supported by the default method.
+}
+
+\usage{
+match(x, table, nomatch=NA_integer_, incomparables=NULL, ...)
+}
+
+\arguments{
+ \item{x, table}{
+ Vector-like R objects (typically of the same class, but not necessarily).
+ }
+ \item{nomatch, incomparables}{
+ See \code{?base::\link[base]{match}} for a description of
+ these arguments.
+ }
+ \item{...}{
+ Additional arguments, for use in specific methods.
+ }
+}
+
+\value{
+ The same as the default method, that is, an integer vector of the same
+ length as \code{x} giving the position in \code{table} of the first match
+ if there is a match, otherwise \code{nomatch}.
+
+ See \code{?base::\link[base]{match}} for more details.
+
+ Specific methods defined in Bioconductor packages should
+ behave as consistently as possible with the default method.
+}
+
+\note{
+ The default method (defined in the base package) doesn't have the
+ \code{...} argument. We've added it to the generic function defined
+ in the BiocGenerics package in order to allow specific methods to
+ support additional arguments if needed.
+}
+
+\seealso{
+ \code{base::\link[base]{match}} for the default \code{match} method.
+
+ \code{\link[methods]{showMethods}} for displaying a summary of the
+ methods defined for a given generic function.
+
+ \code{\link[methods]{selectMethod}} for getting the definition of
+ a specific method.
+
+ \link[IRanges]{match,Hits,Hits-method} in the IRanges
+ package for an example of a specific \code{match} method (defined for
+ \link[IRanges]{Hits} objects).
+
+ \link{BiocGenerics} for a summary of all the generics defined
+ in the BiocGenerics package.
+}
+
+\examples{
+match # note the dispatch on the 'x' and 'table' args only
+showMethods("match")
+selectMethod("match", c("ANY", "ANY")) # the default method
+}
+
+\keyword{methods}
diff --git a/man/nrow.Rd b/man/nrow.Rd
index 5009ab9..21fe274 100644
--- a/man/nrow.Rd
+++ b/man/nrow.Rd
@@ -11,7 +11,7 @@
Return the number of rows or columns present in an array-like R object.
NOTE: This man page is for the \code{nrow}, \code{ncol}, \code{NROW} and
- \code{NCOL} S4 generic functions defined in the BiocGenerics package.
+ \code{NCOL} \emph{S4 generic functions} defined in the BiocGenerics package.
See \code{?base::\link[base]{nrow}} for the default methods (defined in
the base package).
Bioconductor packages can define specific methods for objects
@@ -34,7 +34,7 @@ NCOL(x)
\value{
A single integer or \code{NULL}.
- Specific methods defined in other Bioconductor packages should
+ Specific methods defined in Bioconductor packages should
behave as consistently as possible with the default methods.
}
@@ -49,8 +49,8 @@ NCOL(x)
a specific method.
\link[IRanges]{nrow,DataFrame-method} in the IRanges package
- for the \code{nrow} method defined for \link[IRanges]{DataFrame}
- objects.
+ for an example of a specific \code{nrow} method (defined for
+ \link[IRanges]{DataFrame} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/order.Rd b/man/order.Rd
index ace523c..5829d3c 100644
--- a/man/order.Rd
+++ b/man/order.Rd
@@ -9,7 +9,7 @@
into ascending or descending order, breaking ties by further
arguments.
- NOTE: This man page is for the \code{order} S4 generic function
+ NOTE: This man page is for the \code{order} \emph{S4 generic function}
defined in the BiocGenerics package.
See \code{?base::\link[base]{order}} for the default method
(defined in the base package).
@@ -38,23 +38,29 @@ order(..., na.last=TRUE, decreasing=FALSE)
elements and can be used to rearrange the first argument in
\code{...} into ascending or descending order (by subsetting it).
- Specific methods defined in other Bioconductor packages must also
+ Specific methods defined in Bioconductor packages should also
return an integer vector representing a permutation of N elements.
}
\note{
- TO DEVELOPPERS: Here are 2 common pitfalls when implementing an
- \code{order} method:
- \itemize{
- \item \code{order(x, decreasing=TRUE)} is \emph{not} equivalent
- to \code{rev(order(x))};
- \item It should be made "stable" for consistent behavior across platforms
- and consistency with \code{base::order()}. Note that C qsort() is
- \emph{not} "stable" so \code{order} methods that use qsort() at
- the C-level need to ultimately break ties by position (this is
- generally done by adding a little extra code at the end of the
- comparison function used in the calls to qsort()).
- }
+ TO DEVELOPPERS:
+
+ Specific \code{order} methods should preferably be made "stable" for
+ consistent behavior across platforms and consistency with
+ \code{base::order()}. Note that C qsort() is \emph{not} "stable" so
+ \code{order} methods that use qsort() at the C-level need to ultimately
+ break ties by position, which can easily be done by adding a little
+ extra code at the end of the comparison function passed to qsort().
+
+ \code{order(x, decreasing=TRUE)} is \emph{not} always equivalent to
+ \code{rev(order(x))}.
+
+ \code{\link[BiocGenerics]{order}}, \code{\link[BiocGenerics]{sort}},
+ and \code{\link[BiocGenerics]{rank}} methods for specific vector-like
+ objects should adhere to the same underlying order that should be
+ conceptually defined as a binary relation on the set of all possible
+ vector values. For completeness, this binary relation should also be
+ incarnated by a \link{<=} method.
}
\seealso{
@@ -67,7 +73,8 @@ order(..., na.last=TRUE, decreasing=FALSE)
a specific method.
\link[IRanges]{order,Ranges-method} in the IRanges package
- for the method defined for \link[IRanges]{Ranges} objects.
+ for an example of a specific \code{order} method (defined for
+ \link[IRanges]{Ranges} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/paste.Rd b/man/paste.Rd
index cad124e..c5cfa00 100644
--- a/man/paste.Rd
+++ b/man/paste.Rd
@@ -8,7 +8,7 @@
\code{paste} concatenates vectors of strings or vector-like R
objects containing strings.
- NOTE: This man page is for the \code{paste} S4 generic function
+ NOTE: This man page is for the \code{paste} \emph{S4 generic function}
defined in the BiocGenerics package.
See \code{?base::\link[base]{paste}} for the default method
(defined in the base package).
@@ -35,7 +35,7 @@ paste(..., sep=" ", collapse=NULL)
See \code{?base::\link[base]{paste}} for the value returned by the
default method.
- Specific methods defined in other Bioconductor packages will typically
+ Specific methods defined in Bioconductor packages will typically
return an object of the same class as the input objects.
}
@@ -49,7 +49,8 @@ paste(..., sep=" ", collapse=NULL)
a specific method.
\link[IRanges]{paste,Rle-method} in the IRanges package
- for the method defined for \link[IRanges]{Rle} objects.
+ for an example of a specific \code{paste} method (defined for
+ \link[IRanges]{Rle} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/rank.Rd b/man/rank.Rd
new file mode 100644
index 0000000..3a85bec
--- /dev/null
+++ b/man/rank.Rd
@@ -0,0 +1,80 @@
+\name{rank}
+
+\alias{rank}
+
+\title{Ranks the values in a vector-like object}
+
+\description{
+ Returns the ranks of the values in a vector-like object.
+ Ties (i.e., equal values) and missing values can be handled in several ways.
+
+ NOTE: This man page is for the \code{rank}
+ \emph{S4 generic function} defined in the BiocGenerics package.
+ See \code{?base::\link[base]{rank}} for the default method
+ (defined in the base package).
+ Bioconductor packages can define specific methods for objects
+ not supported by the default method.
+}
+
+\usage{
+rank(x, na.last=TRUE,
+ ties.method=c("average", "first", "random", "max", "min"))
+}
+
+\arguments{
+ \item{x}{
+ A vector-like R object.
+ }
+ \item{na.last, ties.method}{
+ See \code{?base::\link[base]{rank}} for a description of
+ these arguments.
+ }
+}
+
+\value{
+ See \code{?base::\link[base]{rank}} for the value returned
+ by the default method.
+
+ Specific methods defined in Bioconductor packages should
+ behave as consistently as possible with the default method.
+}
+
+\note{
+ TO DEVELOPPERS:
+
+ See note in \code{?BiocGenerics::\link[BiocGenerics]{order}}
+ about "stable" order.
+
+ \code{\link[BiocGenerics]{order}}, \code{\link[BiocGenerics]{sort}},
+ and \code{\link[BiocGenerics]{rank}} methods for specific vector-like
+ objects should adhere to the same underlying order that should be
+ conceptually defined as a binary relation on the set of all possible
+ vector values. For completeness, this binary relation should also be
+ incarnated by a \link{<=} method.
+}
+
+\seealso{
+ \code{base::\link[base]{rank}} for the default
+ \code{rank} method.
+
+ \code{\link[methods]{showMethods}} for displaying a summary of the
+ methods defined for a given generic function.
+
+ \code{\link[methods]{selectMethod}} for getting the definition of
+ a specific method.
+
+ \link[IRanges]{rank,Vector-method} in the IRanges package
+ for an example of a specific \code{rank} method (defined for
+ \link[IRanges]{Vector} objects).
+
+ \link{BiocGenerics} for a summary of all the generics defined
+ in the BiocGenerics package.
+}
+
+\examples{
+rank # note the dispatch on the 'x' arg only
+showMethods("rank")
+selectMethod("rank", "ANY") # the default method
+}
+
+\keyword{methods}
diff --git a/man/rep.Rd b/man/rep.Rd
index 7069b05..7c6b0e5 100644
--- a/man/rep.Rd
+++ b/man/rep.Rd
@@ -7,7 +7,7 @@
\description{
\code{rep.int} replicates the elements in \code{x}.
- NOTE: This man page is for the \code{rep.int} S4 generic function
+ NOTE: This man page is for the \code{rep.int} \emph{S4 generic function}
defined in the BiocGenerics package.
See \code{?base::\link[base]{rep.int}} for the default method
(defined in the base package).
@@ -35,7 +35,7 @@ rep.int(x, ...)
See \code{?base::\link[base]{rep.int}} for the value returned by the
default method.
- Specific methods defined in other Bioconductor packages will typically
+ Specific methods defined in Bioconductor packages will typically
return an object of the same class as the input object.
}
@@ -50,7 +50,8 @@ rep.int(x, ...)
a specific method.
\link[IRanges]{rep.int,Rle-method} in the IRanges package
- for the method defined for \link[IRanges]{Rle} objects.
+ for an example of a specific \code{rep.int} method (defined for
+ \link[IRanges]{Rle} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/residuals.Rd b/man/residuals.Rd
index 33047b9..a2800cf 100644
--- a/man/residuals.Rd
+++ b/man/residuals.Rd
@@ -8,7 +8,7 @@
\code{residuals} is a generic function which extracts model residuals
from objects returned by modeling functions.
- NOTE: This man page is for the \code{residuals} S4 generic function
+ NOTE: This man page is for the \code{residuals} \emph{S4 generic function}
defined in the BiocGenerics package.
See \code{?stats::\link[stats]{residuals}} for the default method
(defined in the stats package).
@@ -41,7 +41,8 @@ residuals(object, ...)
a specific method.
\link[affyPLM]{residuals,PLMset-method} in the affyPLM package
- for the method defined for \link[affyPLM]{PLMset} objects.
+ for an example of a specific \code{residuals} method (defined for
+ \link[affyPLM]{PLMset} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/row_colnames.Rd b/man/row_colnames.Rd
index 94c7923..27bbfe9 100644
--- a/man/row_colnames.Rd
+++ b/man/row_colnames.Rd
@@ -10,7 +10,7 @@
Retrieve the row or column names of a matrix-like R object.
NOTE: This man page is for the \code{rownames} and \code{colnames}
- S4 generic functions defined in the BiocGenerics package.
+ \emph{S4 generic functions} defined in the BiocGenerics package.
See \code{?base::\link[base]{rownames}} for the default methods
(defined in the base package).
Bioconductor packages can define specific methods for objects
@@ -38,7 +38,7 @@ colnames(x, do.NULL=TRUE, prefix="col")
See \code{?base::\link[base]{rownames}} for more information about the
default methods.
- Specific methods defined in other Bioconductor packages should
+ Specific methods defined in Bioconductor packages should
behave as consistently as possible with the default methods.
}
@@ -53,8 +53,8 @@ colnames(x, do.NULL=TRUE, prefix="col")
a specific method.
\link[IRanges]{rownames,DataFrame-method} in the IRanges package
- for the \code{rownames} method defined for \link[IRanges]{DataFrame}
- objects.
+ for an example of a specific \code{rownames} method (defined for
+ \link[IRanges]{DataFrame} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/sets.Rd b/man/sets.Rd
index 6209217..301580c 100644
--- a/man/sets.Rd
+++ b/man/sets.Rd
@@ -12,7 +12,8 @@
on two vector-like R objects.
NOTE: This man page is for the \code{union}, \code{intersect} and
- \code{setdiff} S4 generic functions defined in the BiocGenerics package.
+ \code{setdiff} \emph{S4 generic functions} defined in the BiocGenerics
+ package.
See \code{?base::\link[base]{union}} for the default methods
(defined in the base package).
Bioconductor packages can define specific methods for objects
@@ -34,6 +35,14 @@ setdiff(x, y, ...)
}
}
+\value{
+ See \code{?base::\link[base]{union}} for the value returned by the
+ default methods.
+
+ Specific methods defined in Bioconductor packages will typically
+ return an object of the same class as the input objects.
+}
+
\note{
The default methods (defined in the base package) only take 2 arguments.
We've added the \code{...} argument to the generic functions defined in
@@ -51,14 +60,6 @@ setdiff(x, y, ...)
\code{ignore.strand} argument.)
}
-\value{
- See \code{?base::\link[base]{union}} for the value returned by the
- default methods.
-
- Specific methods defined in other Bioconductor packages will typically
- return an object of the same class as the input objects.
-}
-
\seealso{
\code{base::\link[base]{union}} for the default \code{union},
\code{intersect}, and \code{setdiff} methods.
@@ -70,8 +71,8 @@ setdiff(x, y, ...)
a specific method.
\link[GenomicRanges]{union,GRanges,GRanges-method} in the GenomicRanges
- package for the \code{union} method defined for \link[GenomicRanges]{GRanges}
- objects.
+ package for an example of a specific \code{union} method (defined for
+ \link[GenomicRanges]{GRanges} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/sort.Rd b/man/sort.Rd
new file mode 100644
index 0000000..b58b0ca
--- /dev/null
+++ b/man/sort.Rd
@@ -0,0 +1,78 @@
+\name{sort}
+
+\alias{sort}
+
+\title{Sorting a vector-like object}
+
+\description{
+ Sort a vector-like object into ascending or descending order.
+
+ NOTE: This man page is for the \code{sort}
+ \emph{S4 generic function} defined in the BiocGenerics package.
+ See \code{?base::\link[base]{sort}} for the default method
+ (defined in the base package).
+ Bioconductor packages can define specific methods for objects
+ not supported by the default method.
+}
+
+\usage{
+sort(x, decreasing=FALSE, ...)
+}
+
+\arguments{
+ \item{x}{
+ A vector-like R object.
+ }
+ \item{decreasing, ...}{
+ See \code{?base::\link[base]{sort}} for a description of
+ these arguments.
+ }
+}
+
+\value{
+ See \code{?base::\link[base]{sort}} for the value returned
+ by the default method.
+
+ Specific methods defined in Bioconductor packages should
+ behave as consistently as possible with the default method.
+}
+
+\note{
+ TO DEVELOPPERS:
+
+ See note in \code{?BiocGenerics::\link[BiocGenerics]{order}}
+ about "stable" order.
+
+ \code{\link[BiocGenerics]{order}}, \code{\link[BiocGenerics]{sort}},
+ and \code{\link[BiocGenerics]{rank}} methods for specific vector-like
+ objects should adhere to the same underlying order that should be
+ conceptually defined as a binary relation on the set of all possible
+ vector values. For completeness, this binary relation should also be
+ incarnated by a \link{<=} method.
+}
+
+\seealso{
+ \code{base::\link[base]{sort}} for the default
+ \code{sort} method.
+
+ \code{\link[methods]{showMethods}} for displaying a summary of the
+ methods defined for a given generic function.
+
+ \code{\link[methods]{selectMethod}} for getting the definition of
+ a specific method.
+
+ \link[IRanges]{sort,Vector-method} in the IRanges package
+ for an example of a specific \code{sort} method (defined for
+ \link[IRanges]{Vector} objects).
+
+ \link{BiocGenerics} for a summary of all the generics defined
+ in the BiocGenerics package.
+}
+
+\examples{
+sort # note the dispatch on the 'x' arg only
+showMethods("sort")
+selectMethod("sort", "ANY") # the default method
+}
+
+\keyword{methods}
diff --git a/man/table.Rd b/man/table.Rd
index 7710bc6..5ad7662 100644
--- a/man/table.Rd
+++ b/man/table.Rd
@@ -8,7 +8,7 @@
\code{table} uses the cross-classifying factors to build a contingency
table of the counts at each combination of factor levels.
- NOTE: This man page is for the \code{table} S4 generic function
+ NOTE: This man page is for the \code{table} \emph{S4 generic function}
defined in the BiocGenerics package.
See \code{?base::\link[base]{table}} for the default method
(defined in the base package).
@@ -32,7 +32,7 @@ table(...)
See \code{?base::\link[base]{table}} for the value returned by the
default method.
- Specific methods defined in other Bioconductor packages should also
+ Specific methods defined in Bioconductor packages should also
return the type of object returned by the default method.
}
@@ -46,7 +46,8 @@ table(...)
a specific method.
\link[IRanges]{table,Rle-method} in the IRanges package
- for the method defined for \link[IRanges]{Rle} objects.
+ for an example of a specific \code{table} method (defined
+ for \link[IRanges]{Rle} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/tapply.Rd b/man/tapply.Rd
index 657d980..9554d12 100644
--- a/man/tapply.Rd
+++ b/man/tapply.Rd
@@ -9,7 +9,7 @@
that is to each (non-empty) group of values given by a unique
combination of the levels of certain factors.
- NOTE: This man page is for the \code{tapply} S4 generic function
+ NOTE: This man page is for the \code{tapply} \emph{S4 generic function}
defined in the BiocGenerics package.
See \code{?base::\link[base]{tapply}} for the default method
(defined in the base package).
@@ -36,7 +36,7 @@ tapply(X, INDEX, FUN=NULL, ..., simplify=TRUE)
See \code{?base::\link[base]{tapply}} for the value returned by the
default method.
- Specific methods defined in other Bioconductor packages should
+ Specific methods defined in Bioconductor packages should
behave as consistently as possible with the default method.
}
@@ -50,8 +50,8 @@ tapply(X, INDEX, FUN=NULL, ..., simplify=TRUE)
a specific method.
\link[IRanges]{tapply,Vector-method} in the IRanges package
- for the \code{tapply} method defined for \link[IRanges]{Vector}
- objects.
+ for an example of a specific \code{tapply} method (defined for
+ \link[IRanges]{Vector} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/unique.Rd b/man/unique.Rd
index 1c6f772..0800350 100644
--- a/man/unique.Rd
+++ b/man/unique.Rd
@@ -9,7 +9,7 @@
a vector-like, data-frame-like, or array-like R object) but with duplicate
elements/rows removed.
- NOTE: This man page is for the \code{unique} S4 generic function
+ NOTE: This man page is for the \code{unique} \emph{S4 generic function}
defined in the BiocGenerics package.
See \code{?base::\link[base]{unique}} for the default method
(defined in the base package).
@@ -36,7 +36,7 @@ unique(x, incomparables=FALSE, ...)
See \code{?base::\link[base]{unique}} for the value returned by the
default method.
- Specific methods defined in other Bioconductor packages will typically
+ Specific methods defined in Bioconductor packages will typically
return an object of the same class as the input object.
\code{unique} should always behave consistently with
@@ -55,8 +55,9 @@ unique(x, incomparables=FALSE, ...)
\code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \link[IRanges]{unique,Ranges-method} in the IRanges package
- for the method defined for \link[IRanges]{Ranges} objects.
+ \link[IRanges]{unique,Rle-method} in the IRanges package
+ for an example of a specific \code{unique} method (defined for
+ \link[IRanges]{Rle} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/unlist.Rd b/man/unlist.Rd
new file mode 100644
index 0000000..2a0f153
--- /dev/null
+++ b/man/unlist.Rd
@@ -0,0 +1,67 @@
+\name{unlist}
+
+\alias{unlist}
+
+\title{Flatten list-like objects}
+
+\description{
+ Given a list-like object \code{x}, \code{unlist} produces a vector-like
+ object obtained by concatenating (conceptually thru \code{\link{c}}) all
+ the top-level elements in \code{x} (each of them being expected to be
+ a vector-like object, typically).
+
+ NOTE: This man page is for the \code{unlist}
+ \emph{S4 generic function} defined in the BiocGenerics package.
+ See \code{?base::\link[base]{unlist}} for the default method
+ (defined in the base package).
+ Bioconductor packages can define specific methods for objects
+ not supported by the default method.
+}
+
+\usage{
+unlist(x, recursive=TRUE, use.names=TRUE)
+}
+
+\arguments{
+ \item{x}{
+ A list-like R object.
+ }
+ \item{recursive, use.names}{
+ See \code{?base::\link[base]{unlist}} for a description of
+ these arguments.
+ }
+}
+
+\value{
+ See \code{?base::\link[base]{unlist}} for the value returned
+ by the default method.
+
+ Specific methods defined in Bioconductor packages should
+ behave as consistently as possible with the default method.
+}
+
+\seealso{
+ \code{base::\link[base]{unlist}} for the default
+ \code{unlist} method.
+
+ \code{\link[methods]{showMethods}} for displaying a summary of the
+ methods defined for a given generic function.
+
+ \code{\link[methods]{selectMethod}} for getting the definition of
+ a specific method.
+
+ \link[IRanges]{unlist,List-method} in the IRanges package
+ for an example of a specific \code{unlist} method (defined for
+ \link[IRanges]{List} objects).
+
+ \link{BiocGenerics} for a summary of all the generics defined
+ in the BiocGenerics package.
+}
+
+\examples{
+unlist # note the dispatch on the 'x' arg only
+showMethods("unlist")
+selectMethod("unlist", "ANY") # the default method
+}
+
+\keyword{methods}
diff --git a/man/weights.Rd b/man/weights.Rd
index d2ceb85..e3a67ea 100644
--- a/man/weights.Rd
+++ b/man/weights.Rd
@@ -8,7 +8,7 @@
\code{weights} is a generic function which extracts fitting weights
from objects returned by modeling functions.
- NOTE: This man page is for the \code{weights} S4 generic function
+ NOTE: This man page is for the \code{weights} \emph{S4 generic function}
defined in the BiocGenerics package.
See \code{?stats::\link[stats]{weights}} for the default method
(defined in the stats package).
@@ -32,7 +32,7 @@ weights(object, ...)
See \code{?stats::\link[stats]{weights}} for the value returned by the
default method.
- Specific methods defined in other Bioconductor packages should
+ Specific methods defined in Bioconductor packages should
behave as consistently as possible with the default method.
}
@@ -47,7 +47,8 @@ weights(object, ...)
a specific method.
\link[affyPLM]{weights,PLMset-method} in the affyPLM package
- for the method defined for \link[affyPLM]{PLMset} objects.
+ for an example of a specific \code{weights} method (defined for
+ \link[affyPLM]{PLMset} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
diff --git a/man/xtabs.Rd b/man/xtabs.Rd
index 4e38e84..e7714b6 100644
--- a/man/xtabs.Rd
+++ b/man/xtabs.Rd
@@ -9,7 +9,7 @@
cross-classifying factors, usually contained in a data-frame-like object,
using a formula interface.
- NOTE: This man page is for the \code{xtabs} S4 generic function
+ NOTE: This man page is for the \code{xtabs} \emph{S4 generic function}
defined in the BiocGenerics package.
See \code{?stats::\link[stats]{xtabs}} for the default method
(defined in the stats package).
@@ -36,7 +36,7 @@ xtabs(formula=~., data=parent.frame(), subset, sparse=FALSE,
See \code{?stats::\link[stats]{xtabs}} for the value returned by the
default method.
- Specific methods defined in other Bioconductor packages should also
+ Specific methods defined in Bioconductor packages should also
return the type of object returned by the default method.
}
@@ -50,7 +50,8 @@ xtabs(formula=~., data=parent.frame(), subset, sparse=FALSE,
a specific method.
\link[IRanges]{xtabs,DataTable-method} in the IRanges package
- for the method defined for \link[IRanges]{DataTable} objects.
+ for an example of a specific \code{xtabs} method (defined for
+ \link[IRanges]{DataTable} objects).
\link{BiocGenerics} for a summary of all the generics defined
in the BiocGenerics package.
--
generic functions for Bioconductor
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