[med-svn] [r-bioc-biocgenerics] 01/05: Imported Upstream version 0.10.0
Andreas Tille
tille at debian.org
Tue Jun 10 07:57:30 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-biocgenerics.
commit 9e63e979d9544ea584e1dad12ee88d12636c3152
Author: Andreas Tille <tille at debian.org>
Date: Tue Jun 10 09:54:08 2014 +0200
Imported Upstream version 0.10.0
---
DESCRIPTION | 29 ++++++++--------
NAMESPACE | 26 ++++++++++++--
R/do.call.R | 10 ++++++
R/relist.R | 8 +++++
R/show-utils.R | 4 ++-
R/strand.R | 6 ++++
man/BiocGenerics-package.Rd | 37 ++++++++++++--------
man/Extremes.Rd | 10 +++---
man/S3-classes-as-S4-classes.Rd | 4 +--
man/annotation.Rd | 4 +--
man/append.Rd | 12 +++----
man/as.data.frame.Rd | 14 ++++----
man/as.vector.Rd | 12 +++----
man/boxplot.Rd | 8 ++---
man/cbind.Rd | 8 ++---
man/clusterApply.Rd | 6 ++--
man/combine.Rd | 10 +++---
man/density.Rd | 12 +++----
man/dge.Rd | 2 +-
man/do.call.Rd | 75 +++++++++++++++++++++++++++++++++++++++++
man/duplicated.Rd | 12 +++----
man/eval.Rd | 10 +++---
man/evalq.Rd | 4 +--
man/funprog.Rd | 8 ++---
man/get.Rd | 8 ++---
man/image.Rd | 8 ++---
man/is.unsorted.Rd | 25 ++++++--------
man/lapply.Rd | 8 ++---
man/mapply.Rd | 8 ++---
man/match.Rd | 12 +++----
man/normalize.Rd | 12 +++----
man/nrow.Rd | 9 ++---
man/order.Rd | 8 ++---
man/paste.Rd | 8 ++---
man/plotMA.Rd | 4 +--
man/rank.Rd | 8 ++---
man/relist.Rd | 64 +++++++++++++++++++++++++++++++++++
man/rep.Rd | 8 ++---
man/residuals.Rd | 8 ++---
man/row_colnames.Rd | 12 +++----
man/sets.Rd | 18 +++++-----
man/sort.Rd | 8 ++---
man/strand.Rd | 28 ++++++++++-----
man/table.Rd | 8 ++---
man/tapply.Rd | 31 ++++++++++++-----
man/unique.Rd | 8 ++---
man/unlist.Rd | 8 ++---
man/updateObject.Rd | 6 ++--
man/weights.Rd | 8 ++---
man/xtabs.Rd | 8 ++---
50 files changed, 443 insertions(+), 229 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index ec244f1..e953dc1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,23 +1,22 @@
Package: BiocGenerics
-Title: Generic functions for Bioconductor
+Title: S4 generic functions for Bioconductor
Description: S4 generic functions needed by many Bioconductor packages.
-Version: 0.8.0
+Version: 0.10.0
Author: The Bioconductor Dev Team
-Maintainer: Bioconductor Package Maintainer
- <maintainer at bioconductor.org>
+Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
biocViews: Infrastructure
-Depends: methods, graphics, stats, parallel
-Imports: methods, graphics, stats, parallel
+Depends: methods, utils, graphics, stats, parallel
+Imports: methods, utils, graphics, stats, parallel
Suggests: Biobase, IRanges, GenomicRanges, AnnotationDbi, oligoClasses,
oligo, affyPLM, flowClust, affy, RUnit, DESeq2
License: Artistic-2.0
Collate: S3-classes-as-S4-classes.R append.R as.data.frame.R
- as.vector.R cbind.R dge.R plotMA.R duplicated.R eval.R
- Extremes.R funprog.R get.R is.unsorted.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 normalize.R normarg-utils.R show-utils.R
- strand.R updateObject.R update.R testPackage.R
- test_BiocGenerics_package.R zzz.R
-Packaged: 2013-10-15 04:35:59 UTC; biocbuild
+ as.vector.R cbind.R do.call.R duplicated.R eval.R Extremes.R
+ funprog.R get.R is.unsorted.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 relist.R boxplot.R image.R
+ density.R residuals.R weights.R xtabs.R clusterApply.R
+ annotation.R combine.R dge.R normalize.R plotMA.R
+ normarg-utils.R show-utils.R strand.R updateObject.R update.R
+ testPackage.R test_BiocGenerics_package.R zzz.R
+Packaged: 2014-04-12 06:44:47 UTC; biocbuild
diff --git a/NAMESPACE b/NAMESPACE
index a850e37..ab63c81 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,4 +1,5 @@
import(methods)
+import(utils)
import(graphics)
import(stats)
import(parallel)
@@ -16,8 +17,8 @@ exportClasses(
### ==========================================================================
-### Functions defined in base R and explicitly promoted to generics in the
-### BiocGenerics package
+### Export functions defined in base R and explicitly promoted to generics in
+### the BiocGenerics package
### --------------------------------------------------------------------------
### Generics for functions defined in package base:
@@ -34,6 +35,9 @@ export(
## from R/cbind.R:
cbind, rbind,
+ ## from R/do.call.R:
+ do.call,
+
## from R/duplicated.R:
duplicated, anyDuplicated,
@@ -98,6 +102,12 @@ export(
unlist
)
+### Generics for functions defined in package utils:
+export(
+ ## from R/relist.R:
+ relist
+)
+
### Generics for functions defined in package graphics:
export(
## from R/boxplot.R:
@@ -134,7 +144,7 @@ export(
### ==========================================================================
-### Bioconductor specific generics and their methods
+### Export Bioconductor specific generics and their methods
### --------------------------------------------------------------------------
export(
@@ -175,3 +185,13 @@ exportMethods(
plotMA
)
+
+### ==========================================================================
+### Export non-generic functions
+### --------------------------------------------------------------------------
+
+export(
+ ## from R/strand.R:
+ unstrand
+)
+
diff --git a/R/do.call.R b/R/do.call.R
new file mode 100644
index 0000000..7d17e0e
--- /dev/null
+++ b/R/do.call.R
@@ -0,0 +1,10 @@
+### =========================================================================
+### The do.call() generic
+### -------------------------------------------------------------------------
+
+### Need to explicitly define this generic otherwise the implicit generic in
+### package "base" would dispatch on all its arguments. Here we set dispatch
+### on the 1st and 2nd args only!
+
+setGeneric("do.call", signature=c("what", "args"))
+
diff --git a/R/relist.R b/R/relist.R
new file mode 100644
index 0000000..7e2f875
--- /dev/null
+++ b/R/relist.R
@@ -0,0 +1,8 @@
+### =========================================================================
+### The relist() generic
+### -------------------------------------------------------------------------
+###
+### utils::relist is an S3 generic.
+
+setGeneric("relist")
+
diff --git a/R/show-utils.R b/R/show-utils.R
index 23fee71..58e713f 100644
--- a/R/show-utils.R
+++ b/R/show-utils.R
@@ -6,7 +6,7 @@
labeledLine <-
function(label, els, count = TRUE, labelSep = ":", sep = " ", ellipsis = "...")
{
- if (count)
+ if (count && !is.null(els))
label <- paste(label, "(", length(els), ")", sep = "")
label <- paste(label, labelSep, sep, sep = "")
width <- getOption("width") - nchar(label)
@@ -17,6 +17,8 @@ labeledLine <-
ellipsize <-
function(obj, width = getOption("width"), sep = " ", ellipsis = "...")
{
+ if (is.null(obj))
+ obj <- "NULL"
if (length(obj) > 2 * width)
obj <- c(head(obj, width), tail(obj, width))
str <- encodeString(obj)
diff --git a/R/strand.R b/R/strand.R
index c0d740f..06517c9 100644
--- a/R/strand.R
+++ b/R/strand.R
@@ -6,3 +6,9 @@ setGeneric("strand", function(x, ...) standardGeneric("strand"))
setGeneric("strand<-", function(x, ..., value) standardGeneric("strand<-"))
+unstrand <- function(x)
+{
+ strand(x) <- "*"
+ x
+}
+
diff --git a/man/BiocGenerics-package.Rd b/man/BiocGenerics-package.Rd
index ddbb75f..1654a9a 100644
--- a/man/BiocGenerics-package.Rd
+++ b/man/BiocGenerics-package.Rd
@@ -4,22 +4,22 @@
\alias{BiocGenerics}
\docType{package}
-\title{Generic functions for Bioconductor}
+\title{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
+ We divide the generic functions defined in the \pkg{BiocGenerics} package
+ in 2 categories: (1) functions already defined in base R and explicitly
promoted to generics in BiocGenerics, and (2) Bioconductor specific
generics.
\subsection{(1) Functions defined in base R and explicitly promoted to
- generics in the BiocGenerics package}{
+ generics in the \pkg{BiocGenerics} package}{
- Generics for functions defined in package base:
+ Generics for functions defined in package \pkg{base}:
\itemize{
\item \code{BiocGenerics::\link[BiocGenerics]{append}}
@@ -30,6 +30,8 @@
\item \code{BiocGenerics::\link[BiocGenerics]{cbind}},
\code{BiocGenerics::\link[BiocGenerics]{rbind}}
+ \item \code{BiocGenerics::\link[BiocGenerics]{do.call}}
+
\item \code{BiocGenerics::\link[BiocGenerics]{duplicated}},
\code{BiocGenerics::\link[BiocGenerics]{anyDuplicated}}
@@ -51,6 +53,8 @@
\item \code{BiocGenerics::\link[BiocGenerics]{get}},
\code{BiocGenerics::\link[BiocGenerics]{mget}}
+ \item \code{BiocGenerics::\link[BiocGenerics]{is.unsorted}}
+
\item \code{BiocGenerics::\link[BiocGenerics]{lapply}},
\code{BiocGenerics::\link[BiocGenerics]{sapply}}
@@ -90,14 +94,19 @@
\item \code{BiocGenerics::\link[BiocGenerics]{unlist}}
}
- Generics for functions defined in package graphics:
+ Generics for functions defined in package \pkg{utils}:
+ \itemize{
+ \item \code{BiocGenerics::\link[BiocGenerics]{relist}}
+ }
+
+ Generics for functions defined in package \pkg{graphics}:
\itemize{
\item \code{BiocGenerics::\link[BiocGenerics]{boxplot}}
\item \code{BiocGenerics::\link[BiocGenerics]{image}}
}
- Generics for functions defined in package stats:
+ Generics for functions defined in package \pkg{stats}:
\itemize{
\item \code{BiocGenerics::\link[BiocGenerics]{density}}
@@ -108,7 +117,7 @@
\item \code{BiocGenerics::\link[BiocGenerics]{xtabs}}
}
- Generics for functions defined in package parallel:
+ Generics for functions defined in package \pkg{parallel}:
\itemize{
\item \code{BiocGenerics::\link[BiocGenerics]{clusterCall}},
\code{BiocGenerics::\link[BiocGenerics]{clusterApply}},
@@ -150,22 +159,22 @@
\url{http://bioconductor.org/help/mailing-list/}
- Things that should NOT be added to the BiocGenerics package:
+ Things that should NOT be added to the \pkg{BiocGenerics} package:
\itemize{
\item Internal generic primitive functions like \code{\link{length}},
\code{\link{dim}}, \code{`\link{dim<-}`}, etc...
See \code{?\link{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
+ There are a few exceptions though, that is, the \pkg{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 \code{BiocGenerics::\link[BiocGenerics]{cbind}}).
\item S3 and S4 group generic functions like \code{\link{Math}},
\code{\link{Ops}}, etc... See \code{?\link{groupGeneric}} and
\code{?\link{S4groupGeneric}} for the complete list.
- \item Generics already defined in the stats4 package.
+ \item Generics already defined in the \pkg{stats4} package.
}
}
diff --git a/man/Extremes.Rd b/man/Extremes.Rd
index 944b697..6a233fa 100644
--- a/man/Extremes.Rd
+++ b/man/Extremes.Rd
@@ -13,10 +13,10 @@
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} \emph{S4 generic functions} defined in the BiocGenerics
- package.
+ and \code{pmin.int} \emph{S4 generic functions} defined in the
+ \pkg{BiocGenerics} package.
See \code{?base::\link[base]{pmax}} for the default methods
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically vector-like or matrix-like) not supported by the default
methods.
@@ -59,12 +59,12 @@ pmin.int(..., na.rm=FALSE)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{pmax,Rle-method} in the IRanges package
+ \item \link[IRanges]{pmax,Rle-method} in the \pkg{IRanges} package
for an example of a specific \code{pmax} method (defined for
\link[IRanges]{Rle} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/S3-classes-as-S4-classes.Rd b/man/S3-classes-as-S4-classes.Rd
index f2ab1fc..e608a05 100644
--- a/man/S3-classes-as-S4-classes.Rd
+++ b/man/S3-classes-as-S4-classes.Rd
@@ -25,7 +25,7 @@
\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
+ classes by the \pkg{BiocGenerics} package. This allows S4 methods defined in
Bioconductor packages to use them in their signatures.
}
@@ -45,7 +45,7 @@
}
\seealso{
- \link{setOldClass} and \link{setClassUnion} in the methods package.
+ \link{setOldClass} and \link{setClassUnion} in the \pkg{methods} package.
}
\keyword{classes}
diff --git a/man/annotation.Rd b/man/annotation.Rd
index 9073eea..4718b33 100644
--- a/man/annotation.Rd
+++ b/man/annotation.Rd
@@ -34,12 +34,12 @@ annotation(object, ...) <- value
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[Biobase]{annotation,eSet-method} in the Biobase package
+ \item \link[Biobase]{annotation,eSet-method} in the \pkg{Biobase} package
for an example of a specific \code{annotation} method (defined for
\link[Biobase]{eSet} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/append.Rd b/man/append.Rd
index 9e6e36a..6185016 100644
--- a/man/append.Rd
+++ b/man/append.Rd
@@ -8,9 +8,9 @@
Append (or insert) elements to (in) a vector-like object.
NOTE: This man page is for the \code{append} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{append}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically vector-like or data-frame-like) not supported by the
default method.
@@ -54,12 +54,12 @@ append(x, values, after=length(x))
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{append,Vector,Vector-method} in the IRanges package
- for an example of a specific \code{append} method (defined for
- \link[IRanges]{Vector} objects).
+ \item \link[IRanges]{append,Vector,Vector-method} in the \pkg{IRanges}
+ package for an example of a specific \code{append} method (defined
+ for \link[IRanges]{Vector} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/as.data.frame.Rd b/man/as.data.frame.Rd
index 55e1f3e..e6edf84 100644
--- a/man/as.data.frame.Rd
+++ b/man/as.data.frame.Rd
@@ -8,9 +8,9 @@
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.
+ \emph{S4 generic function} defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{as.data.frame}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
not supported by the default method.
}
@@ -51,13 +51,13 @@ as.data.frame(x, row.names=NULL, optional=FALSE, ...)
a specific method.
\item \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[IRanges]{as.data.frame,DataFrame-method} in the \pkg{IRanges}
+ package for examples of specific \code{as.data.frame} methods
+ (defined for \link[IRanges]{Ranges} and \link[IRanges]{DataFrame}
+ objects, respectively).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/as.vector.Rd b/man/as.vector.Rd
index 763a4c8..5a546d7 100644
--- a/man/as.vector.Rd
+++ b/man/as.vector.Rd
@@ -11,9 +11,9 @@
object.
NOTE: This man page is for the \code{as.vector}
- \emph{S4 generic function} defined in the BiocGenerics package.
+ \emph{S4 generic function} defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{as.vector}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
not supported by the default method.
}
@@ -54,13 +54,13 @@ as.vector(x, mode="any")
a specific method.
\item \link[IRanges]{as.vector,Rle-method} and
- \link[IRanges]{as.vector,AtomicList-method} in the IRanges package
- for examples of specific \code{as.vector} methods (defined for
- \link[IRanges]{Rle} and \link[IRanges]{AtomicList} objects,
+ \link[IRanges]{as.vector,AtomicList-method} in the \pkg{IRanges}
+ package for examples of specific \code{as.vector} methods (defined
+ for \link[IRanges]{Rle} and \link[IRanges]{AtomicList} objects,
respectively).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/boxplot.Rd b/man/boxplot.Rd
index 4a1cbb0..784c106 100644
--- a/man/boxplot.Rd
+++ b/man/boxplot.Rd
@@ -8,9 +8,9 @@
Produce box-and-whisker plot(s) of the given (grouped) values.
NOTE: This man page is for the \code{boxplot} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?graphics::\link[graphics]{boxplot}} for the default method
- (defined in the graphics package).
+ (defined in the \pkg{graphics} package).
Bioconductor packages can define specific methods for objects
not supported by the default method.
}
@@ -44,12 +44,12 @@ boxplot(x, ...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[oligo]{boxplot,FeatureSet-method} in the oligo package
+ \item \link[oligo]{boxplot,FeatureSet-method} in the \pkg{oligo} package
for an example of a specific \code{boxplot} method (defined for
\link[oligoClasses]{FeatureSet} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/cbind.Rd b/man/cbind.Rd
index bfdf9b8..94bf284 100644
--- a/man/cbind.Rd
+++ b/man/cbind.Rd
@@ -10,9 +10,9 @@
by columns or rows, respectively.
NOTE: This man page is for the \code{cbind} and \code{rbind}
- \emph{S4 generic functions} defined in the BiocGenerics package.
+ \emph{S4 generic functions} defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{cbind}} for the default methods
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically vector-like or matrix-like) not supported by the default
methods.
@@ -53,12 +53,12 @@ rbind(..., deparse.level=1)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{cbind,DataFrame-method} in the IRanges package
+ \item \link[IRanges]{cbind,DataFrame-method} in the \pkg{IRanges} package
for an example of a specific \code{cbind} method (defined for
\link[IRanges]{DataFrame} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/clusterApply.Rd b/man/clusterApply.Rd
index 833d882..59a6ef6 100644
--- a/man/clusterApply.Rd
+++ b/man/clusterApply.Rd
@@ -26,9 +26,9 @@
\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.
+ \pkg{BiocGenerics} package.
See \code{?parallel::\link[parallel]{clusterApply}} for the default
- methods (defined in the parallel package).
+ methods (defined in the \pkg{parallel} package).
Bioconductor packages can define specific methods for cluster-like
objects not supported by the default methods.
}
@@ -97,7 +97,7 @@ parSapplyLB(cl=NULL, X, FUN, ..., simplify=TRUE, USE.NAMES=TRUE)
a specific method.
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/combine.Rd b/man/combine.Rd
index 0ba2a0d..acaefe6 100644
--- a/man/combine.Rd
+++ b/man/combine.Rd
@@ -41,7 +41,7 @@ combine(x, y, ...)
}
\section{Methods}{
- The following methods are defined in the BiocGenerics package:
+ The following methods are defined in the \pkg{BiocGenerics} package:
\describe{
\item{\code{combine(x=ANY, missing)}}{Return the first (x) argument
unchanged.}
@@ -65,7 +65,7 @@ combine(x, y, ...)
operation, \code{combine} makes sure that data in shared rows and
columns are all equal in the two matricies.}
}
- Additional \code{combine} methods are defined in the Biobase package
+ Additional \code{combine} methods are defined in the \pkg{Biobase} package
for \link[Biobase]{AnnotatedDataFrame},
\link[Biobase]{AssayData}, \link[Biobase]{MIAME},
and \link[Biobase]{eSet} objects.
@@ -84,8 +84,8 @@ combine(x, y, ...)
\item \link[Biobase]{combine,AnnotatedDataFrame,AnnotatedDataFrame-method},
\link[Biobase]{combine,AssayData,AssayData-method},
\link[Biobase]{combine,MIAME,MIAME-method},
- and \link[Biobase]{combine,eSet,eSet-method} in the Biobase package
- for additional \code{combine} methods.
+ and \link[Biobase]{combine,eSet,eSet-method} in the \pkg{Biobase}
+ package for additional \code{combine} methods.
\item \code{\link{merge}} for merging two data frames (or data.frame-like)
objects.
@@ -97,7 +97,7 @@ combine(x, y, ...)
a specific method.
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/density.Rd b/man/density.Rd
index 747af78..09030c7 100644
--- a/man/density.Rd
+++ b/man/density.Rd
@@ -9,9 +9,9 @@
estimates.
NOTE: This man page is for the \code{density} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?stats::\link[stats]{density}} for the default method
- (defined in the stats package).
+ (defined in the \pkg{stats} package).
Bioconductor packages can define specific methods for objects
not supported by the default method.
}
@@ -45,12 +45,12 @@ density(x, ...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[flowClust]{density,flowClust-method} in the flowClust package
- for an example of a specific \code{density} method (defined for
- \link[flowClust]{flowClust} objects).
+ \item \link[flowClust]{density,flowClust-method} in the \pkg{flowClust}
+ package for an example of a specific \code{density} method (defined
+ for \link[flowClust]{flowClust} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/dge.Rd b/man/dge.Rd
index 4061fd9..df84417 100644
--- a/man/dge.Rd
+++ b/man/dge.Rd
@@ -43,7 +43,7 @@ plotDispEsts(object, ...)
}
\details{For the details, please consult the manual pages of the
- methods in the \code{DESeq}, \code{DESeq2}, and \code{DEXSeq} packages and the package
+ methods in the \pkg{DESeq}, \pkg{DESeq2}, and \pkg{DEXSeq} packages and the package
vignettes.}
\author{W. Huber, S. Anders}
diff --git a/man/do.call.Rd b/man/do.call.Rd
new file mode 100644
index 0000000..7ef489d
--- /dev/null
+++ b/man/do.call.Rd
@@ -0,0 +1,75 @@
+\name{do.call}
+
+\alias{do.call}
+
+\title{Execute a function call}
+
+\description{
+ \code{do.call} constructs and executes a function call from a name or a
+ function and a list of arguments to be passed to it.
+
+ NOTE: This man page is for the \code{do.call} \emph{S4 generic function}
+ defined in the \pkg{BiocGenerics} package.
+ See \code{?base::\link[base]{do.call}} for the default method
+ (defined in the \pkg{base} package).
+ Bioconductor packages can define specific methods for objects
+ not supported by the default method.
+}
+
+\usage{
+do.call(what, args, quote=FALSE, envir=parent.frame())
+}
+
+\arguments{
+ \item{what}{
+ The default method expects either a function or a non-empty character
+ string naming the function to be called.
+ See \code{?base::\link[base]{do.call}} for the details.
+
+ Specific methods can support other objects.
+ Please refer to the documentation of a particular method for the details.
+ }
+ \item{args}{
+ The default method expects a \emph{list} of arguments to the function
+ call (the \code{names} attribute of \code{args} gives the argument names).
+ See \code{?base::\link[base]{do.call}} for the details.
+
+ Specific methods can support other objects.
+ Please refer to the documentation of a particular method for the details.
+ }
+ \item{quote, envir}{
+ See \code{?base::\link[base]{do.call}} for a description of
+ these arguments.
+ }
+}
+
+\value{
+ The result of the (evaluated) function call.
+
+ Specific methods defined in Bioconductor packages should
+ behave as consistently as possible with the default method.
+}
+
+\seealso{
+ \itemize{
+ \item \code{base::\link[base]{do.call}} for the default \code{do.call}
+ method.
+
+ \item \code{\link[methods]{showMethods}} for displaying a summary of the
+ methods defined for a given generic function.
+
+ \item \code{\link[methods]{selectMethod}} for getting the definition of
+ a specific method.
+
+ \item \link{BiocGenerics} for a summary of all the generics defined
+ in the \pkg{BiocGenerics} package.
+ }
+}
+
+\examples{
+do.call # note the dispatch on the 'what' and 'args' args only
+showMethods("do.call")
+selectMethod("do.call", c("ANY", "ANY")) # the default method
+}
+
+\keyword{methods}
diff --git a/man/duplicated.Rd b/man/duplicated.Rd
index 95a12c4..b759e94 100644
--- a/man/duplicated.Rd
+++ b/man/duplicated.Rd
@@ -11,9 +11,9 @@
logical vector indicating which elements (rows) are duplicates.
NOTE: This man page is for the \code{duplicated} and \code{anyDuplicated}
- \emph{S4 generic functions} defined in the BiocGenerics package.
+ \emph{S4 generic functions} defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{duplicated}} for the default methods
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically vector-like or data-frame-like) not supported by the
default method.
@@ -69,12 +69,12 @@ anyDuplicated(x, incomparables=FALSE, ...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{duplicated,Ranges-method} in the IRanges package
- for an example of a specific \code{duplicated} method (defined for
- \link[IRanges]{Ranges} objects).
+ \item \link[IRanges]{duplicated,Ranges-method} in the \pkg{IRanges}
+ package for an example of a specific \code{duplicated} method
+ (defined for \link[IRanges]{Ranges} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/eval.Rd b/man/eval.Rd
index e5d5a27..0acee3d 100644
--- a/man/eval.Rd
+++ b/man/eval.Rd
@@ -8,9 +8,9 @@
\code{eval} evaluates an R expression in a specified environment.
NOTE: This man page is for the \code{eval} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{eval}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
not supported by the default method.
}
@@ -58,14 +58,14 @@ eval(expr, envir=parent.frame(),
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{eval,expression,List-method} in the IRanges package
- for an example of a specific \code{eval} method (defined for
+ \item \link[IRanges]{eval,expression,List-method} in the \pkg{IRanges}
+ 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).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/evalq.Rd b/man/evalq.Rd
index 94bc538..7e2ad19 100644
--- a/man/evalq.Rd
+++ b/man/evalq.Rd
@@ -9,8 +9,8 @@
argument) in a specified environment.
NOTE: This man page is for the \code{evalq} wrapper defined in the
- BiocGenerics package. See \code{?base::\link[base]{evalq}} for the
- function defined in the base package. This wrapper correctly delegates
+ \pkg{BiocGenerics} package. See \code{?base::\link[base]{evalq}} for the
+ function defined in the \pkg{base} package. This wrapper correctly delegates
to the \code{eval} generic, rather than
\code{base::\link[base]{eval}}.
}
diff --git a/man/funprog.Rd b/man/funprog.Rd
index f733572..b624676 100644
--- a/man/funprog.Rd
+++ b/man/funprog.Rd
@@ -22,9 +22,9 @@
NOTE: This man page is for the \code{Reduce}, \code{Filter},
\code{Find}, \code{Map} and \code{Position} \emph{S4 generic functions}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{Reduce}} for the default methods
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically list-like or vector-like) not supported by the
default methods.
@@ -70,12 +70,12 @@ Position(f, x, right=FALSE, nomatch=NA_integer_)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{Reduce,List-method} in the IRanges package
+ \item \link[IRanges]{Reduce,List-method} in the \pkg{IRanges} package
for an example of a specific \code{Reduce} method (defined for
\link[IRanges]{List} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/get.Rd b/man/get.Rd
index df492e5..fbbce98 100644
--- a/man/get.Rd
+++ b/man/get.Rd
@@ -9,9 +9,9 @@
Search for an object with a given name and return it.
NOTE: This man page is for the \code{get} and \code{mget} \emph{S4 generic
- functions} defined in the BiocGenerics package.
+ functions} defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{get}} for the default methods
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(list-like or environment-like) not supported by the default methods.
}
@@ -65,11 +65,11 @@ mget(x, envir, mode="any", ifnotfound, inherits=FALSE)
a specific method.
\item \link[AnnotationDbi]{get,ANY,Bimap,missing-method} in the
- AnnotationDbi package for an example of a specific \code{get}
+ \pkg{AnnotationDbi} package for an example of a specific \code{get}
method (defined for \link[AnnotationDbi]{Bimap} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/image.Rd b/man/image.Rd
index 63e7256..6882adf 100644
--- a/man/image.Rd
+++ b/man/image.Rd
@@ -11,9 +11,9 @@
\emph{images}.
NOTE: This man page is for the \code{image} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?graphics::\link[graphics]{image}} for the default method
- (defined in the graphics package).
+ (defined in the \pkg{graphics} package).
Bioconductor packages can define specific methods for objects
not supported by the default method.
}
@@ -46,12 +46,12 @@ image(x, ...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[oligo]{image,FeatureSet-method} in the oligo package
+ \item \link[oligo]{image,FeatureSet-method} in the \pkg{oligo} package
for an example of a specific \code{image} method (defined for
\link[oligoClasses]{FeatureSet} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/is.unsorted.Rd b/man/is.unsorted.Rd
index 3a8fab8..d7c1e62 100644
--- a/man/is.unsorted.Rd
+++ b/man/is.unsorted.Rd
@@ -2,21 +2,21 @@
\alias{is.unsorted}
-\title{Test if an Object is Not Sorted}
+\title{Test if a vector-like object is not sorted}
\description{
- Test if an object is not sorted, without the cost of sorting it.
+ Test if a vector-like object is not sorted, without the cost of sorting it.
NOTE: This man page is for the \code{is.unsorted}
- \emph{S4 generic function} defined in the BiocGenerics package.
+ \emph{S4 generic function} defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{is.unsorted}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
not supported by the default method.
}
\usage{
-is.unsorted(x, na.rm = FALSE, strictly = FALSE)
+is.unsorted(x, na.rm=FALSE, strictly=FALSE)
}
\arguments{
@@ -40,15 +40,10 @@ is.unsorted(x, na.rm = FALSE, strictly = FALSE)
\note{
TO DEVELOPPERS:
- See note in \code{?BiocGenerics::\link[BiocGenerics]{order}}
- about "stable" order.
-
+ The \code{is.unsorted} method for specific vector-like objects should
+ adhere to the same underlying order used by the
\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.
+ and \code{\link[BiocGenerics]{rank}} methods for the same objects.
}
\seealso{
@@ -62,12 +57,12 @@ is.unsorted(x, na.rm = FALSE, strictly = FALSE)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{is.unsorted,Rle-method} in the IRanges package
+ \item \link[IRanges]{is.unsorted,Rle-method} in the \pkg{IRanges} package
for an example of a specific \code{is.unsorted} method (defined for
\link[IRanges]{Rle} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/lapply.Rd b/man/lapply.Rd
index 615d346..49dce22 100644
--- a/man/lapply.Rd
+++ b/man/lapply.Rd
@@ -17,9 +17,9 @@
as \code{lapply(x, f)}.
NOTE: This man page is for the \code{lapply} and \code{sapply}
- \emph{S4 generic functions} defined in the BiocGenerics package.
+ \emph{S4 generic functions} defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{lapply}} for the default methods
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically list-like or vector-like) not supported by the
default methods.
@@ -61,12 +61,12 @@ sapply(X, FUN, ..., simplify=TRUE, USE.NAMES=TRUE)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{lapply,List-method} in the IRanges package
+ \item \link[IRanges]{lapply,List-method} in the \pkg{IRanges} package
for an example of a specific \code{lapply} method (defined for
\link[IRanges]{List} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/mapply.Rd b/man/mapply.Rd
index 441ef0c..b8766e7 100644
--- a/man/mapply.Rd
+++ b/man/mapply.Rd
@@ -12,9 +12,9 @@
are recycled if necessary.
NOTE: This man page is for the \code{mapply} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{mapply}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically list-like or vector-like) not supported by the
default methods.
@@ -54,12 +54,12 @@ mapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE, USE.NAMES=TRUE)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{mapply,List-method} in the IRanges package
+ \item \link[IRanges]{mapply,List-method} in the \pkg{IRanges} package
for an example of a specific \code{mapply} method (defined for
\link[IRanges]{List} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/match.Rd b/man/match.Rd
index bd9c8c7..c626655 100644
--- a/man/match.Rd
+++ b/man/match.Rd
@@ -9,9 +9,9 @@
its first argument in its second.
NOTE: This man page is for the \code{match} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{match}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically vector-like) not supported by the default method.
}
@@ -45,9 +45,9 @@ match(x, table, nomatch=NA_integer_, incomparables=NULL, ...)
}
\note{
- The default method (defined in the base package) doesn't have the
+ The default method (defined in the \pkg{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
+ in the \pkg{BiocGenerics} package in order to allow specific methods to
support additional arguments if needed.
}
@@ -61,12 +61,12 @@ match(x, table, nomatch=NA_integer_, incomparables=NULL, ...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{match,Hits,Hits-method} in the IRanges package
+ \item \link[IRanges]{match,Hits,Hits-method} in the \pkg{IRanges} package
for an example of a specific \code{match} method (defined for
\link[IRanges]{Hits} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/normalize.Rd b/man/normalize.Rd
index 922b6b1..15cefbe 100644
--- a/man/normalize.Rd
+++ b/man/normalize.Rd
@@ -38,14 +38,14 @@ normalize(object, ...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[affy]{normalize,AffyBatch-method} in the affy package
- and \link[oligo]{normalize,FeatureSet-method} in the oligo package
- for examples of specific \code{normalize} methods (defined for
- \link[affy]{AffyBatch} and \link[oligoClasses]{FeatureSet} objects,
- respectively).
+ \item \link[affy]{normalize,AffyBatch-method} in the \pkg{affy} package
+ and \link[oligo]{normalize,FeatureSet-method} in the \pkg{oligo}
+ package for examples of specific \code{normalize} methods (defined
+ for \link[affy]{AffyBatch} and \link[oligoClasses]{FeatureSet}
+ objects, respectively).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/nrow.Rd b/man/nrow.Rd
index 2127448..3afa5c3 100644
--- a/man/nrow.Rd
+++ b/man/nrow.Rd
@@ -11,9 +11,10 @@
Return the number of rows or columns present in an array-like object.
NOTE: This man page is for the \code{nrow}, \code{ncol}, \code{NROW} and
- \code{NCOL} \emph{S4 generic functions} defined in the BiocGenerics package.
+ \code{NCOL} \emph{S4 generic functions} defined in the \pkg{BiocGenerics}
+ package.
See \code{?base::\link[base]{nrow}} for the default methods (defined in
- the base package).
+ the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically matrix- or array-like) not supported by the default methods.
}
@@ -49,12 +50,12 @@ NCOL(x)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{nrow,DataFrame-method} in the IRanges package
+ \item \link[IRanges]{nrow,DataFrame-method} in the \pkg{IRanges} package
for an example of a specific \code{nrow} method (defined for
\link[IRanges]{DataFrame} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/order.Rd b/man/order.Rd
index d8d1801..47ed5ca 100644
--- a/man/order.Rd
+++ b/man/order.Rd
@@ -10,9 +10,9 @@
arguments.
NOTE: This man page is for the \code{order} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{order}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically vector-like) not supported by the default method.
}
@@ -73,12 +73,12 @@ order(..., na.last=TRUE, decreasing=FALSE)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{order,Ranges-method} in the IRanges package
+ \item \link[IRanges]{order,Ranges-method} in the \pkg{IRanges} package
for an example of a specific \code{order} method (defined for
\link[IRanges]{Ranges} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/paste.Rd b/man/paste.Rd
index 8ffcab1..e3e958c 100644
--- a/man/paste.Rd
+++ b/man/paste.Rd
@@ -9,9 +9,9 @@
objects containing strings.
NOTE: This man page is for the \code{paste} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{paste}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically vector-like objects containing strings) not supported by
the default method.
@@ -49,12 +49,12 @@ paste(..., sep=" ", collapse=NULL)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{paste,Rle-method} in the IRanges package
+ \item \link[IRanges]{paste,Rle-method} in the \pkg{IRanges} package
for an example of a specific \code{paste} method (defined for
\link[IRanges]{Rle} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/plotMA.Rd b/man/plotMA.Rd
index a44a4cc..6f97cd0 100644
--- a/man/plotMA.Rd
+++ b/man/plotMA.Rd
@@ -35,11 +35,11 @@ plotMA(object, ...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \code{\link[limma]{plotMA}} in the \code{limma} package
+ \item \code{\link[limma]{plotMA}} in the \pkg{limma} package
for a function with the same name that is not dispatched through this generic function.
\item \code{\link{BiocGenerics}} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/rank.Rd b/man/rank.Rd
index 61d2c34..465e2be 100644
--- a/man/rank.Rd
+++ b/man/rank.Rd
@@ -9,9 +9,9 @@
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.
+ \emph{S4 generic function} defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{rank}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
not supported by the default method.
}
@@ -63,12 +63,12 @@ rank(x, na.last=TRUE,
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{rank,Ranges-method} in the IRanges package
+ \item \link[IRanges]{rank,Ranges-method} in the \pkg{IRanges} package
for an example of a specific \code{rank} method (defined for
\link[IRanges]{Ranges} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/relist.Rd b/man/relist.Rd
new file mode 100644
index 0000000..8bf1ac7
--- /dev/null
+++ b/man/relist.Rd
@@ -0,0 +1,64 @@
+\name{relist}
+
+\alias{relist}
+
+\title{Re-listing an unlist()ed object}
+
+\description{
+ \code{relist} is a generic function with a few methods in order to allow
+ easy inversion of \code{unlist(x)}.
+
+ NOTE: This man page is for the \code{relist} \emph{S4 generic function}
+ defined in the \pkg{BiocGenerics} package.
+ See \code{?utils::\link[utils]{relist}} for the default method
+ (defined in the \pkg{utils} package).
+ Bioconductor packages can define specific methods for objects
+ not supported by the default method.
+}
+
+\usage{
+relist(flesh, skeleton)
+}
+
+\arguments{
+ \item{flesh}{
+ A vector-like object.
+ }
+ \item{skeleton}{
+ A list-like object. Only the "shape" (i.e. the lengths of the individual
+ list elements) of \code{skeleton} matters. Its exact content is ignored.
+ }
+}
+
+\value{
+ A list-like object with the same "shape" as \code{skeleton} and that would
+ give \code{flesh} back if unlist()ed.
+}
+
+\seealso{
+ \itemize{
+ \item \code{utils::\link[utils]{relist}} for the default \code{relist}
+ method.
+
+ \item \code{\link[methods]{showMethods}} for displaying a summary of the
+ methods defined for a given generic function.
+
+ \item \code{\link[methods]{selectMethod}} for getting the definition of
+ a specific method.
+
+ \item \link[IRanges]{relist,ANY,List-method} in the \pkg{IRanges} package
+ for an example of a specific \code{relist} method (defined for
+ when \code{skeleton} is a \link[IRanges]{List} object).
+
+ \item \link{BiocGenerics} for a summary of all the generics defined
+ in the \pkg{BiocGenerics} package.
+ }
+}
+
+\examples{
+relist
+showMethods("relist")
+selectMethod("relist", c("ANY", "ANY")) # the default method
+}
+
+\keyword{methods}
diff --git a/man/rep.Rd b/man/rep.Rd
index 55a2517..69f3a75 100644
--- a/man/rep.Rd
+++ b/man/rep.Rd
@@ -8,9 +8,9 @@
\code{rep.int} replicates the elements in \code{x}.
NOTE: This man page is for the \code{rep.int} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{rep.int}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically vector-like) not supported by the default method.
}
@@ -50,12 +50,12 @@ rep.int(x, ...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{rep.int,Rle-method} in the IRanges package
+ \item \link[IRanges]{rep.int,Rle-method} in the \pkg{IRanges} package
for an example of a specific \code{rep.int} method (defined for
\link[IRanges]{Rle} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/residuals.Rd b/man/residuals.Rd
index 2e6399e..93a6371 100644
--- a/man/residuals.Rd
+++ b/man/residuals.Rd
@@ -9,9 +9,9 @@
from objects returned by modeling functions.
NOTE: This man page is for the \code{residuals} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?stats::\link[stats]{residuals}} for the default method
- (defined in the stats package).
+ (defined in the \pkg{stats} package).
Bioconductor packages can define specific methods for objects
not supported by the default method.
}
@@ -41,12 +41,12 @@ residuals(object, ...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[affyPLM]{residuals,PLMset-method} in the affyPLM package
+ \item \link[affyPLM]{residuals,PLMset-method} in the \pkg{affyPLM} package
for an example of a specific \code{residuals} method (defined for
\link[affyPLM]{PLMset} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/row_colnames.Rd b/man/row_colnames.Rd
index b87fdf8..e937c26 100644
--- a/man/row_colnames.Rd
+++ b/man/row_colnames.Rd
@@ -10,9 +10,9 @@
Retrieve the row or column names of a matrix-like object.
NOTE: This man page is for the \code{rownames} and \code{colnames}
- \emph{S4 generic functions} defined in the BiocGenerics package.
+ \emph{S4 generic functions} defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{rownames}} for the default methods
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically matrix-like) not supported by the default methods.
}
@@ -53,12 +53,12 @@ colnames(x, do.NULL=TRUE, prefix="col")
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{rownames,DataFrame-method} in the IRanges package
- for an example of a specific \code{rownames} method (defined for
- \link[IRanges]{DataFrame} objects).
+ \item \link[IRanges]{rownames,DataFrame-method} in the \pkg{IRanges}
+ package for an example of a specific \code{rownames} method (defined
+ for \link[IRanges]{DataFrame} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/sets.Rd b/man/sets.Rd
index f84faee..50cf11a 100644
--- a/man/sets.Rd
+++ b/man/sets.Rd
@@ -12,10 +12,10 @@
on two vector-like objects.
NOTE: This man page is for the \code{union}, \code{intersect} and
- \code{setdiff} \emph{S4 generic functions} defined in the BiocGenerics
+ \code{setdiff} \emph{S4 generic functions} defined in the \pkg{BiocGenerics}
package.
See \code{?base::\link[base]{union}} for the default methods
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically vector-like) not supported by the default methods.
}
@@ -44,10 +44,10 @@ setdiff(x, y, ...)
}
\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
- the BiocGenerics package so they can be called with an arbitrary number
- of effective arguments.
+ The default methods (defined in the \pkg{base} package) only take 2
+ arguments. We've added the \code{...} argument to the generic functions
+ defined in the \pkg{BiocGenerics} package so they can be called with an
+ arbitrary number of effective arguments.
For \code{union} or \code{intersect}, this typically allows Bioconductor
packages to define methods that compute the union or intersection of more
than 2 objects. However, for \code{setdiff}, which is conceptually a
@@ -55,7 +55,7 @@ setdiff(x, y, ...)
for controlling/altering the behavior of the operation.
Like for example the \code{ignore.strand} argument supported by the
\code{setdiff} method for \link[GenomicRanges]{GRanges} objects (defined
- in the GenomicRanges package). (Note that the \code{union} and
+ in the \pkg{GenomicRanges} package). (Note that the \code{union} and
\code{intersect} methods for those objects also support the
\code{ignore.strand} argument.)
}
@@ -72,11 +72,11 @@ setdiff(x, y, ...)
a specific method.
\item \link[GenomicRanges]{union,GRanges,GRanges-method} in the
- GenomicRanges package for an example of a specific \code{union}
+ \pkg{GenomicRanges} package for an example of a specific \code{union}
method (defined for \link[GenomicRanges]{GRanges} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/sort.Rd b/man/sort.Rd
index ad52ab8..472d48f 100644
--- a/man/sort.Rd
+++ b/man/sort.Rd
@@ -8,9 +8,9 @@
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.
+ \emph{S4 generic function} defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{sort}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
not supported by the default method.
}
@@ -62,12 +62,12 @@ sort(x, decreasing=FALSE, ...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{sort,Vector-method} in the IRanges package
+ \item \link[IRanges]{sort,Vector-method} in the \pkg{IRanges} package
for an example of a specific \code{sort} method (defined for
\link[IRanges]{Vector} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/strand.Rd b/man/strand.Rd
index f5fdb54..a900899 100644
--- a/man/strand.Rd
+++ b/man/strand.Rd
@@ -2,6 +2,7 @@
\alias{strand}
\alias{strand<-}
+\alias{unstrand}
\title{Accessing strand information}
@@ -12,6 +13,7 @@
\usage{
strand(x, ...)
strand(x, ...) <- value
+unstrand(x)
}
\arguments{
@@ -26,15 +28,24 @@ strand(x, ...) <- value
}
}
-\note{
- All the \code{strand} methods defined in the GenomicRanges package
- use the same set of 3 values (levels) to specify the strand of a
- genomic location: \code{+}, \code{-}, and \code{*}.
+\details{
+ All the \code{strand} methods defined in the \pkg{GenomicRanges} package
+ use the same set of 3 values (called the "standard strand levels") to
+ specify the strand of a genomic location: \code{+}, \code{-}, and \code{*}.
\code{*} is used when the exact strand of the location is unknown,
or irrelevant, or when the "feature" at that location belongs to
both strands.
}
+\note{
+ \code{unstrand} is not a generic function, just a convenience wrapper to
+ the generic strand setter (\code{strand<-}) that simply does:
+\preformatted{
+ strand(x) <- "*"
+ x
+}
+}
+
\seealso{
\itemize{
\item \code{\link[methods]{showMethods}} for displaying a summary of the
@@ -43,12 +54,13 @@ strand(x, ...) <- value
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[GenomicRanges]{strand,GRanges-method} in the GenomicRanges
- package for an example of a specific \code{strand} method (defined
- for \link[GenomicRanges]{GRanges} objects).
+ \item \link[GenomicRanges]{strand,GRanges-method} in the
+ \pkg{GenomicRanges} package for an example of a specific
+ \code{strand} method (defined for \link[GenomicRanges]{GRanges}
+ objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/table.Rd b/man/table.Rd
index 6421b91..064e4d3 100644
--- a/man/table.Rd
+++ b/man/table.Rd
@@ -9,9 +9,9 @@
table of the counts at each combination of factor levels.
NOTE: This man page is for the \code{table} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{table}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
not supported by the default method.
}
@@ -46,12 +46,12 @@ table(...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{table,Rle-method} in the IRanges package
+ \item \link[IRanges]{table,Rle-method} in the \pkg{IRanges} package
for an example of a specific \code{table} method (defined for
\link[IRanges]{Rle} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/tapply.Rd b/man/tapply.Rd
index 8510857..762b4b1 100644
--- a/man/tapply.Rd
+++ b/man/tapply.Rd
@@ -10,12 +10,12 @@
combination of the levels of certain factors.
NOTE: This man page is for the \code{tapply} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{tapply}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically list-like or vector-like) not supported by the
- default methods.
+ default method.
}
\usage{
@@ -24,9 +24,22 @@ tapply(X, INDEX, FUN=NULL, ..., simplify=TRUE)
\arguments{
\item{X}{
- A list-like or vector-like object.
+ The default method expects an atomic object, typically a vector.
+ See \code{?base::\link[base]{tapply}} for the details.
+
+ Specific methods can support other objects (typically list-like
+ or vector-like).
+ Please refer to the documentation of a particular method for the details.
+ }
+ \item{INDEX}{
+ The default method expects a list of one or more factors, each of same
+ length as \code{X}.
+ See \code{?base::\link[base]{tapply}} for the details.
+
+ Specific methods can support other objects (typically list-like).
+ Please refer to the documentation of a particular method for the details.
}
- \item{INDEX, FUN, ..., simplify}{
+ \item{FUN, ..., simplify}{
See \code{?base::\link[base]{tapply}} for a description of
these arguments.
}
@@ -51,19 +64,19 @@ tapply(X, INDEX, FUN=NULL, ..., simplify=TRUE)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{tapply,Vector-method} in the IRanges package
+ \item \link[IRanges]{tapply,Vector,ANY-method} in the \pkg{IRanges} package
for an example of a specific \code{tapply} method (defined for
\link[IRanges]{Vector} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
\examples{
-tapply # note the dispatch on the 'X' arg only
+tapply # note the dispatch on the 'X' and 'INDEX' args only
showMethods("tapply")
-selectMethod("tapply", "ANY") # the default method
+selectMethod("tapply", c("ANY", "ANY")) # the default method
}
\keyword{methods}
diff --git a/man/unique.Rd b/man/unique.Rd
index 0e6a5d0..badd689 100644
--- a/man/unique.Rd
+++ b/man/unique.Rd
@@ -10,9 +10,9 @@
elements/rows removed.
NOTE: This man page is for the \code{unique} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{unique}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically vector-like or data-frame-like) not supported by the
default method.
@@ -57,12 +57,12 @@ unique(x, incomparables=FALSE, ...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{unique,Rle-method} in the IRanges package
+ \item \link[IRanges]{unique,Rle-method} in the \pkg{IRanges} package
for an example of a specific \code{unique} method (defined for
\link[IRanges]{Rle} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/unlist.Rd b/man/unlist.Rd
index ffd120b..b40350a 100644
--- a/man/unlist.Rd
+++ b/man/unlist.Rd
@@ -11,9 +11,9 @@
a vector-like object, typically).
NOTE: This man page is for the \code{unlist}
- \emph{S4 generic function} defined in the BiocGenerics package.
+ \emph{S4 generic function} defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{unlist}} for the default method
- (defined in the base package).
+ (defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
not supported by the default method.
}
@@ -51,12 +51,12 @@ unlist(x, recursive=TRUE, use.names=TRUE)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{unlist,List-method} in the IRanges package
+ \item \link[IRanges]{unlist,List-method} in the \pkg{IRanges} package
for an example of a specific \code{unlist} method (defined for
\link[IRanges]{List} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/updateObject.Rd b/man/updateObject.Rd
index 47154c2..27c7e18 100644
--- a/man/updateObject.Rd
+++ b/man/updateObject.Rd
@@ -108,8 +108,8 @@ getObjectSlots(object)
\seealso{
\itemize{
- \item \code{\link[Biobase]{updateObjectTo}} in the Biobase package for
- updating an object to the class definition of a template (might
+ \item \code{\link[Biobase]{updateObjectTo}} in the \pkg{Biobase} package
+ for updating an object to the class definition of a template (might
be useful for updating a virtual superclass).
\item \code{\link[methods]{validObject}} for testing the validity of an
@@ -122,7 +122,7 @@ getObjectSlots(object)
a specific method.
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/weights.Rd b/man/weights.Rd
index ce9ab9c..66385ac 100644
--- a/man/weights.Rd
+++ b/man/weights.Rd
@@ -9,9 +9,9 @@
from objects returned by modeling functions.
NOTE: This man page is for the \code{weights} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?stats::\link[stats]{weights}} for the default method
- (defined in the stats package).
+ (defined in the \pkg{stats} package).
Bioconductor packages can define specific methods for objects
not supported by the default method.
}
@@ -47,12 +47,12 @@ weights(object, ...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[affyPLM]{weights,PLMset-method} in the affyPLM package
+ \item \link[affyPLM]{weights,PLMset-method} in the \pkg{affyPLM} package
for an example of a specific \code{weights} method (defined for
\link[affyPLM]{PLMset} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
diff --git a/man/xtabs.Rd b/man/xtabs.Rd
index 96a467b..64352ee 100644
--- a/man/xtabs.Rd
+++ b/man/xtabs.Rd
@@ -10,9 +10,9 @@
using a formula interface.
NOTE: This man page is for the \code{xtabs} \emph{S4 generic function}
- defined in the BiocGenerics package.
+ defined in the \pkg{BiocGenerics} package.
See \code{?stats::\link[stats]{xtabs}} for the default method
- (defined in the stats package).
+ (defined in the \pkg{stats} package).
Bioconductor packages can define specific methods for objects
not supported by the default method.
}
@@ -51,12 +51,12 @@ xtabs(formula=~., data=parent.frame(), subset, sparse=FALSE,
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{xtabs,DataTable-method} in the IRanges package
+ \item \link[IRanges]{xtabs,DataTable-method} in the \pkg{IRanges} package
for an example of a specific \code{xtabs} method (defined for
\link[IRanges]{DataTable} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
- in the BiocGenerics package.
+ in the \pkg{BiocGenerics} package.
}
}
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-biocgenerics.git
More information about the debian-med-commit
mailing list