[med-svn] [r-bioc-biocgenerics] 01/07: Imported Upstream version 0.12.0
Andreas Tille
tille at debian.org
Wed Oct 15 22:09:51 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 52b69ed1ab2ba2066769f0e1c4fd6f084e74059d
Author: Andreas Tille <tille at debian.org>
Date: Wed Oct 15 23:47:29 2014 +0200
Imported Upstream version 0.12.0
---
DESCRIPTION | 20 ++++-----
NAMESPACE | 15 ++++++-
R/as.list.R | 4 ++
R/row_colnames.R | 9 ++--
R/start.R | 25 +++++++++++
R/unsplit.R | 10 +++++
man/BiocGenerics-package.Rd | 11 ++++-
man/Extremes.Rd | 4 +-
man/append.Rd | 4 +-
man/as.data.frame.Rd | 9 ++--
man/as.vector.Rd | 10 ++---
man/cbind.Rd | 6 +--
man/duplicated.Rd | 4 +-
man/eval.Rd | 4 +-
man/funprog.Rd | 4 +-
man/is.unsorted.Rd | 6 +--
man/lapply.Rd | 4 +-
man/mapply.Rd | 4 --
man/match.Rd | 6 +--
man/nrow.Rd | 6 +--
man/paste.Rd | 4 +-
man/relist.Rd | 6 +--
man/rep.Rd | 4 +-
man/row_colnames.Rd | 45 ++++++++++++++-----
man/sort.Rd | 4 +-
man/start.Rd | 104 ++++++++++++++++++++++++++++++++++++++++++++
man/table.Rd | 4 +-
man/tapply.Rd | 6 +--
man/unique.Rd | 4 +-
man/unlist.Rd | 4 +-
man/unsplit.Rd | 72 ++++++++++++++++++++++++++++++
man/xtabs.Rd | 6 +--
32 files changed, 344 insertions(+), 84 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index e953dc1..290cafb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,22 +1,22 @@
Package: BiocGenerics
Title: S4 generic functions for Bioconductor
Description: S4 generic functions needed by many Bioconductor packages.
-Version: 0.10.0
+Version: 0.12.0
Author: The Bioconductor Dev Team
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
biocViews: Infrastructure
Depends: methods, utils, graphics, stats, parallel
Imports: methods, utils, graphics, stats, parallel
-Suggests: Biobase, IRanges, GenomicRanges, AnnotationDbi, oligoClasses,
- oligo, affyPLM, flowClust, affy, RUnit, DESeq2
+Suggests: Biobase, S4Vectors, 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
+Collate: S3-classes-as-S4-classes.R append.R as.data.frame.R as.list.R
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
+ start.R table.R tapply.R unique.R unlist.R unsplit.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: 2014-10-14 02:25:08 UTC; biocbuild
diff --git a/NAMESPACE b/NAMESPACE
index ab63c81..b5f2522 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -29,6 +29,9 @@ export(
## from R/as.data.frame.R:
as.data.frame,
+ ## from R/as.list.R:
+ as.list,
+
## from R/as.vector.R:
as.vector,
@@ -81,7 +84,7 @@ export(
rep.int,
## from R/row_colnames.R:
- rownames, colnames,
+ rownames, "rownames<-", colnames, "colnames<-",
## from R/sets.R:
union, intersect, setdiff,
@@ -89,6 +92,11 @@ export(
## from R/sort.R:
sort,
+ ## from R/start.R:
+ start, "start<-",
+ end, "end<-",
+ width, "width<-",
+
## from R/table.R:
table,
@@ -99,7 +107,10 @@ export(
unique,
## from R/unlist.R:
- unlist
+ unlist,
+
+ ## from R/unsplit.R:
+ unsplit
)
### Generics for functions defined in package utils:
diff --git a/R/as.list.R b/R/as.list.R
new file mode 100644
index 0000000..1c71b9a
--- /dev/null
+++ b/R/as.list.R
@@ -0,0 +1,4 @@
+
+
+setGeneric("as.list")
+
diff --git a/R/row_colnames.R b/R/row_colnames.R
index 92d9979..db56de7 100644
--- a/R/row_colnames.R
+++ b/R/row_colnames.R
@@ -2,11 +2,14 @@
### The rownames() and colnames() generics
### -------------------------------------------------------------------------
###
-### Need to explicitly define those generics otherwise the implicit generics
-### in package "base" would dispatch on 'do.NULL' and 'prefix'. Here we set
-### dispatch on the 1st arg (the 'x' arg) only!
+### Dispatch on the 1st arg (the 'x' arg) only!
setGeneric("rownames", signature="x")
+setGeneric("rownames<-")
+
+### Dispatch on the 1st arg (the 'x' arg) only!
setGeneric("colnames", signature="x")
+setGeneric("colnames<-")
+
diff --git a/R/start.R b/R/start.R
new file mode 100644
index 0000000..0115dff
--- /dev/null
+++ b/R/start.R
@@ -0,0 +1,25 @@
+### =========================================================================
+### The start(), `start<-`(), end(), `end<-`(), width(), and `width<-`()
+### generics
+### -------------------------------------------------------------------------
+###
+### stats::start and stats::end are S3 generics.
+
+setGeneric("start")
+
+setGeneric("start<-", signature="x",
+ function(x, ..., value) standardGeneric("start<-")
+)
+
+setGeneric("end")
+
+setGeneric("end<-", signature="x",
+ function(x, ..., value) standardGeneric("end<-")
+)
+
+setGeneric("width", function(x) standardGeneric("width"))
+
+setGeneric("width<-", signature="x",
+ function(x, ..., value) standardGeneric("width<-")
+)
+
diff --git a/R/unsplit.R b/R/unsplit.R
new file mode 100644
index 0000000..9a4ea24
--- /dev/null
+++ b/R/unsplit.R
@@ -0,0 +1,10 @@
+### =========================================================================
+### The unsplit() generic
+### -------------------------------------------------------------------------
+###
+### unsplit should not dispatch on 'drop'
+
+setGeneric("unsplit",
+ function (value, f, drop = FALSE) standardGeneric("unsplit"),
+ signature=c("value", "f"))
+
diff --git a/man/BiocGenerics-package.Rd b/man/BiocGenerics-package.Rd
index 1654a9a..c887bc3 100644
--- a/man/BiocGenerics-package.Rd
+++ b/man/BiocGenerics-package.Rd
@@ -76,7 +76,9 @@
\item \code{BiocGenerics::\link[BiocGenerics]{rep.int}}
\item \code{BiocGenerics::\link[BiocGenerics]{rownames}},
- \code{BiocGenerics::\link[BiocGenerics]{colnames}}
+ \code{BiocGenerics::\link[BiocGenerics]{rownames<-}},
+ \code{BiocGenerics::\link[BiocGenerics]{colnames}},
+ \code{BiocGenerics::\link[BiocGenerics]{colnames<-}}
\item sets:
\code{BiocGenerics::\link[BiocGenerics]{union}},
@@ -85,6 +87,13 @@
\item \code{BiocGenerics::\link[BiocGenerics]{sort}}
+ \item \code{BiocGenerics::\link[BiocGenerics]{start}},
+ \code{BiocGenerics::\link[BiocGenerics]{start<-}},
+ \code{BiocGenerics::\link[BiocGenerics]{end}},
+ \code{BiocGenerics::\link[BiocGenerics]{end<-}},
+ \code{BiocGenerics::\link[BiocGenerics]{width}},
+ \code{BiocGenerics::\link[BiocGenerics]{width<-}}
+
\item \code{BiocGenerics::\link[BiocGenerics]{table}}
\item \code{BiocGenerics::\link[BiocGenerics]{tapply}}
diff --git a/man/Extremes.Rd b/man/Extremes.Rd
index 6a233fa..15cbe95 100644
--- a/man/Extremes.Rd
+++ b/man/Extremes.Rd
@@ -59,9 +59,9 @@ 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 \pkg{IRanges} package
+ \item \link[S4Vectors]{pmax,Rle-method} in the \pkg{S4Vectors} package
for an example of a specific \code{pmax} method (defined for
- \link[IRanges]{Rle} objects).
+ \link[S4Vectors]{Rle} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/append.Rd b/man/append.Rd
index 6185016..cd2b64a 100644
--- a/man/append.Rd
+++ b/man/append.Rd
@@ -54,9 +54,9 @@ 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 \pkg{IRanges}
+ \item \link[S4Vectors]{append,Vector,Vector-method} in the \pkg{S4Vectors}
package for an example of a specific \code{append} method (defined
- for \link[IRanges]{Vector} objects).
+ for \link[S4Vectors]{Vector} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/as.data.frame.Rd b/man/as.data.frame.Rd
index e6edf84..0090b5f 100644
--- a/man/as.data.frame.Rd
+++ b/man/as.data.frame.Rd
@@ -50,10 +50,11 @@ as.data.frame(x, row.names=NULL, optional=FALSE, ...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{as.data.frame,Ranges-method} and
- \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}
+ \item \link[S4Vectors]{as.data.frame,DataFrame-method} in the
+ \pkg{S4Vectors} package, and
+ \link[IRanges]{as.data.frame,Ranges-method} in the \pkg{IRanges}
+ package, for examples of specific \code{as.data.frame} methods
+ (defined for \link[S4Vectors]{DataFrame} and \link[IRanges]{Ranges}
objects, respectively).
\item \link{BiocGenerics} for a summary of all the generics defined
diff --git a/man/as.vector.Rd b/man/as.vector.Rd
index 5a546d7..70aa081 100644
--- a/man/as.vector.Rd
+++ b/man/as.vector.Rd
@@ -53,11 +53,11 @@ as.vector(x, mode="any")
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{as.vector,Rle-method} and
- \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[S4Vectors]{as.vector,Rle-method} and
+ \link[IRanges]{as.vector,AtomicList-method} in the \pkg{S4Vectors}
+ and \pkg{IRanges} packages, respectively, for examples of specific
+ \code{as.vector} methods (defined for \link[S4Vectors]{Rle} and
+ \link[IRanges]{AtomicList} objects, respectively).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/cbind.Rd b/man/cbind.Rd
index 94bf284..6399258 100644
--- a/man/cbind.Rd
+++ b/man/cbind.Rd
@@ -53,9 +53,9 @@ 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 \pkg{IRanges} package
- for an example of a specific \code{cbind} method (defined for
- \link[IRanges]{DataFrame} objects).
+ \item \link[IRanges]{cbind,DataFrame-method} in the \pkg{IRanges}
+ package for an example of a specific \code{cbind} method (defined
+ for \link[S4Vectors]{DataFrame} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/duplicated.Rd b/man/duplicated.Rd
index b759e94..69af653 100644
--- a/man/duplicated.Rd
+++ b/man/duplicated.Rd
@@ -69,9 +69,9 @@ 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 \pkg{IRanges}
+ \item \link[S4Vectors]{duplicated,Rle-method} in the \pkg{S4Vectors}
package for an example of a specific \code{duplicated} method
- (defined for \link[IRanges]{Ranges} objects).
+ (defined for \link[S4Vectors]{Rle} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/eval.Rd b/man/eval.Rd
index 0acee3d..9becc59 100644
--- a/man/eval.Rd
+++ b/man/eval.Rd
@@ -58,10 +58,10 @@ 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 \pkg{IRanges}
+ \item \link[IRanges]{eval,expression,Vector-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,
+ \link[base]{expression} and a \link[S4Vectors]{Vector} object,
respectively).
\item \link{BiocGenerics} for a summary of all the generics defined
diff --git a/man/funprog.Rd b/man/funprog.Rd
index b624676..b2c4d77 100644
--- a/man/funprog.Rd
+++ b/man/funprog.Rd
@@ -70,9 +70,9 @@ 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 \pkg{IRanges} package
+ \item \link[S4Vectors]{Reduce,List-method} in the \pkg{S4Vectors} package
for an example of a specific \code{Reduce} method (defined for
- \link[IRanges]{List} objects).
+ \link[S4Vectors]{List} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/is.unsorted.Rd b/man/is.unsorted.Rd
index d7c1e62..71364c9 100644
--- a/man/is.unsorted.Rd
+++ b/man/is.unsorted.Rd
@@ -57,9 +57,9 @@ 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 \pkg{IRanges} package
- for an example of a specific \code{is.unsorted} method (defined for
- \link[IRanges]{Rle} objects).
+ \item \link[S4Vectors]{is.unsorted,Rle-method} in the \pkg{S4Vectors}
+ package for an example of a specific \code{is.unsorted} method
+ (defined for \link[S4Vectors]{Rle} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/lapply.Rd b/man/lapply.Rd
index 49dce22..be9aad0 100644
--- a/man/lapply.Rd
+++ b/man/lapply.Rd
@@ -61,9 +61,9 @@ 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 \pkg{IRanges} package
+ \item \link[S4Vectors]{lapply,List-method} in the \pkg{S4Vectors} package
for an example of a specific \code{lapply} method (defined for
- \link[IRanges]{List} objects).
+ \link[S4Vectors]{List} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/mapply.Rd b/man/mapply.Rd
index b8766e7..5766572 100644
--- a/man/mapply.Rd
+++ b/man/mapply.Rd
@@ -54,10 +54,6 @@ 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 \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 \pkg{BiocGenerics} package.
}
diff --git a/man/match.Rd b/man/match.Rd
index c626655..b68be46 100644
--- a/man/match.Rd
+++ b/man/match.Rd
@@ -61,9 +61,9 @@ 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 \pkg{IRanges} package
- for an example of a specific \code{match} method (defined for
- \link[IRanges]{Hits} objects).
+ \item \link[S4Vectors]{match,Hits,Hits-method} in the \pkg{S4Vectors}
+ package for an example of a specific \code{match} method (defined
+ for \link[S4Vectors]{Hits} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/nrow.Rd b/man/nrow.Rd
index 3afa5c3..cdb4bda 100644
--- a/man/nrow.Rd
+++ b/man/nrow.Rd
@@ -50,9 +50,9 @@ NCOL(x)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \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[S4Vectors]{nrow,DataFrame-method} in the \pkg{S4Vectors}
+ package for an example of a specific \code{nrow} method (defined
+ for \link[S4Vectors]{DataFrame} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/paste.Rd b/man/paste.Rd
index e3e958c..656d7d9 100644
--- a/man/paste.Rd
+++ b/man/paste.Rd
@@ -49,9 +49,9 @@ 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 \pkg{IRanges} package
+ \item \link[S4Vectors]{paste,Rle-method} in the \pkg{S4Vectors} package
for an example of a specific \code{paste} method (defined for
- \link[IRanges]{Rle} objects).
+ \link[S4Vectors]{Rle} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/relist.Rd b/man/relist.Rd
index 8bf1ac7..efd9117 100644
--- a/man/relist.Rd
+++ b/man/relist.Rd
@@ -46,9 +46,9 @@ relist(flesh, skeleton)
\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[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[S4Vectors]{List} object).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/rep.Rd b/man/rep.Rd
index 69f3a75..ec5a17a 100644
--- a/man/rep.Rd
+++ b/man/rep.Rd
@@ -50,9 +50,9 @@ 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 \pkg{IRanges} package
+ \item \link[S4Vectors]{rep.int,Rle-method} in the \pkg{S4Vectors} package
for an example of a specific \code{rep.int} method (defined for
- \link[IRanges]{Rle} objects).
+ \link[S4Vectors]{Rle} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/row_colnames.Rd b/man/row_colnames.Rd
index e937c26..5121563 100644
--- a/man/row_colnames.Rd
+++ b/man/row_colnames.Rd
@@ -2,15 +2,18 @@
\alias{row+colnames}
\alias{rownames}
+\alias{rownames<-}
\alias{colnames}
+\alias{colnames<-}
\title{Row and column names}
\description{
- Retrieve the row or column names of a matrix-like object.
+ Get or set 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 \pkg{BiocGenerics} package.
+ NOTE: This man page is for the \code{rownames}, \code{`rownames<-`},
+ \code{colnames}, and \code{`colnames<-`} \emph{S4 generic functions}
+ defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{rownames}} for the default methods
(defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
@@ -19,7 +22,10 @@
\usage{
rownames(x, do.NULL=TRUE, prefix="row")
+rownames(x) <- value
+
colnames(x, do.NULL=TRUE, prefix="col")
+colnames(x) <- value
}
\arguments{
@@ -30,13 +36,19 @@ colnames(x, do.NULL=TRUE, prefix="col")
See \code{?base::\link[base]{rownames}} for a description of
these arguments.
}
+ \item{value}{
+ Either \code{NULL} or a character vector equal of length equal to the
+ appropriate dimension.
+ }
}
\value{
- \code{NULL} or a character vector of length \code{\link{nrow}(x)}
- for \code{rownames} and \code{\link{ncol}(x)} for \code{colnames(x)}.
+ The getters will return \code{NULL} or a character vector of length
+ \code{\link{nrow}(x)} for \code{rownames} and length \code{\link{ncol}(x)}
+ for \code{colnames(x)}.
+
See \code{?base::\link[base]{rownames}} for more information about the
- default methods.
+ default methods, including how the setters are expected to behave.
Specific methods defined in Bioconductor packages should
behave as consistently as possible with the default methods.
@@ -44,8 +56,9 @@ colnames(x, do.NULL=TRUE, prefix="col")
\seealso{
\itemize{
- \item \code{base::\link[base]{rownames}} for the default \code{rownames}
- and \code{colnames} methods.
+ \item \code{base::\link[base]{rownames}} for the default \code{rownames},
+ \code{`rownames<-`}, \code{colnames}, and \code{`colnames<-`}
+ methods.
\item \code{\link[methods]{showMethods}} for displaying a summary of the
methods defined for a given generic function.
@@ -53,9 +66,9 @@ 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 \pkg{IRanges}
+ \item \link[S4Vectors]{rownames,DataFrame-method} in the \pkg{S4Vectors}
package for an example of a specific \code{rownames} method (defined
- for \link[IRanges]{DataFrame} objects).
+ for \link[S4Vectors]{DataFrame} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
@@ -63,13 +76,25 @@ colnames(x, do.NULL=TRUE, prefix="col")
}
\examples{
+## rownames getter:
rownames # note the dispatch on the 'x' arg only
showMethods("rownames")
selectMethod("rownames", "ANY") # the default method
+## rownames setter:
+`rownames<-`
+showMethods("rownames<-")
+selectMethod("rownames<-", "ANY") # the default method
+
+## colnames getter:
colnames # note the dispatch on the 'x' arg only
showMethods("colnames")
selectMethod("colnames", "ANY") # the default method
+
+## colnames setter:
+`colnames<-`
+showMethods("colnames<-")
+selectMethod("colnames<-", "ANY") # the default method
}
\keyword{methods}
diff --git a/man/sort.Rd b/man/sort.Rd
index 472d48f..d26124e 100644
--- a/man/sort.Rd
+++ b/man/sort.Rd
@@ -62,9 +62,9 @@ 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 \pkg{IRanges} package
+ \item \link[S4Vectors]{sort,Vector-method} in the \pkg{S4Vectors} package
for an example of a specific \code{sort} method (defined for
- \link[IRanges]{Vector} objects).
+ \link[S4Vectors]{Vector} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/start.Rd b/man/start.Rd
new file mode 100644
index 0000000..6c0c78b
--- /dev/null
+++ b/man/start.Rd
@@ -0,0 +1,104 @@
+\name{start}
+
+\alias{start}
+\alias{start<-}
+\alias{end}
+\alias{end<-}
+\alias{width}
+\alias{width<-}
+
+\title{Start, end, width generic getters and setters}
+
+\description{
+ Get or set the start, end, or width of an object.
+
+ NOTE: This man page is for the \code{start}, \code{`start<-`},
+ \code{end}, \code{`end<-`}, \code{width}, and \code{`width<-`}
+ \emph{S4 generic functions} defined in the \pkg{BiocGenerics} package.
+ See \code{?stats::\link[stats]{start}} for the \code{start} and \code{end}
+ S3 generics defined in the \pkg{stats} package.
+}
+
+\usage{
+start(x, ...)
+start(x, ...) <- value
+
+end(x, ...)
+end(x, ...) <- value
+
+width(x)
+width(x, ...) <- value
+}
+
+\arguments{
+ \item{x}{
+ An object containing start, end, and width values.
+ }
+ \item{...}{
+ Additional arguments, for use in specific methods.
+ }
+ \item{value}{
+ The start, end, or width values to set on \code{x}.
+ }
+}
+
+\value{
+ See specific methods defined in Bioconductor packages.
+}
+
+\seealso{
+ \itemize{
+ \item \code{stats::\link[stats]{start}} in the \pkg{stats} package
+ for the \code{start} and \code{end} S3 generics.
+
+ \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]{start,IRanges-method} in the \pkg{IRanges}
+ package for examples of specific \code{start}, \code{end}, and
+ \code{width} methods (defined for \link[IRanges]{IRanges} objects).
+
+ \item \link{BiocGenerics} for a summary of all the generics defined
+ in the \pkg{BiocGenerics} package.
+ }
+}
+
+\examples{
+## start getter:
+start
+showMethods("start")
+
+library(IRanges)
+showMethods("start")
+selectMethod("start", "IRanges") # start getter for IRanges objects
+
+## start setter:
+`start<-`
+showMethods("start<-")
+selectMethod("start<-", "IRanges") # start setter for IRanges objects
+
+## end getter:
+end
+showMethods("end")
+selectMethod("end", "IRanges") # end getter for IRanges objects
+
+## end setter:
+`end<-`
+showMethods("end<-")
+selectMethod("end<-", "IRanges") # end setter for IRanges objects
+
+## width getter:
+width
+showMethods("width")
+selectMethod("width", "IRanges") # width getter for IRanges objects
+
+## width setter:
+`width<-`
+showMethods("width<-")
+selectMethod("width<-", "IRanges") # width setter for IRanges objects
+}
+
+\keyword{methods}
diff --git a/man/table.Rd b/man/table.Rd
index 064e4d3..e55f738 100644
--- a/man/table.Rd
+++ b/man/table.Rd
@@ -46,9 +46,9 @@ table(...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[IRanges]{table,Rle-method} in the \pkg{IRanges} package
+ \item \link[S4Vectors]{table,Rle-method} in the \pkg{S4Vectors} package
for an example of a specific \code{table} method (defined for
- \link[IRanges]{Rle} objects).
+ \link[S4Vectors]{Rle} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/tapply.Rd b/man/tapply.Rd
index 762b4b1..f7fb50e 100644
--- a/man/tapply.Rd
+++ b/man/tapply.Rd
@@ -64,9 +64,9 @@ 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,ANY-method} in the \pkg{IRanges} package
- for an example of a specific \code{tapply} method (defined for
- \link[IRanges]{Vector} objects).
+ \item \link[IRanges]{tapply,Vector,ANY-method} in the \pkg{IRanges}
+ package for an example of a specific \code{tapply} method (defined
+ for \link[S4Vectors]{Vector} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/unique.Rd b/man/unique.Rd
index badd689..e20932b 100644
--- a/man/unique.Rd
+++ b/man/unique.Rd
@@ -57,9 +57,9 @@ 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 \pkg{IRanges} package
+ \item \link[S4Vectors]{unique,Rle-method} in the \pkg{S4Vectors} package
for an example of a specific \code{unique} method (defined for
- \link[IRanges]{Rle} objects).
+ \link[S4Vectors]{Rle} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/unlist.Rd b/man/unlist.Rd
index b40350a..f72253b 100644
--- a/man/unlist.Rd
+++ b/man/unlist.Rd
@@ -51,9 +51,9 @@ 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 \pkg{IRanges} package
+ \item \link[S4Vectors]{unlist,List-method} in the \pkg{S4Vectors} package
for an example of a specific \code{unlist} method (defined for
- \link[IRanges]{List} objects).
+ \link[S4Vectors]{List} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/unsplit.Rd b/man/unsplit.Rd
new file mode 100644
index 0000000..7f84ac2
--- /dev/null
+++ b/man/unsplit.Rd
@@ -0,0 +1,72 @@
+\name{unsplit}
+
+\alias{unsplit}
+
+\title{Unsplit a list-like object}
+
+\description{
+ Given a list-like object \code{value} and grouping \code{f},
+ \code{unsplit} produces a vector-like object \code{x} by conceptually
+ reversing the split operation \code{value <- split(x, f)}.
+
+ NOTE: This man page is for the \code{unsplit}
+ \emph{S4 generic function} defined in the \pkg{BiocGenerics} package.
+ See \code{?base::\link[base]{unsplit}} 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{
+unsplit(x, recursive=TRUE, use.names=TRUE)
+}
+
+\arguments{
+ \item{value}{
+ A list-like object.
+ }
+ \item{f}{
+ A factor or other grouping object that corresponds to the \code{f}
+ symbol in \code{value <- split(x, f)}.
+ }
+ \item{drop}{
+ See \code{?base::\link[base]{unsplit}} for a description of
+ this argument.
+ }
+}
+
+\value{
+ See \code{?base::\link[base]{unsplit}} 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{
+ \itemize{
+ \item \code{base::\link[base]{unsplit}} for the default
+ \code{unsplit} 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]{unsplit,List-method} in the \pkg{IRanges} package
+ for an example of a specific \code{unsplit} method (defined for
+ \link[S4Vectors]{List} objects).
+
+ \item \link{BiocGenerics} for a summary of all the generics defined
+ in the \pkg{BiocGenerics} package.
+ }
+}
+
+\examples{
+unsplit # note the dispatch on the 'value' and 'f' args only
+showMethods("unsplit")
+selectMethod("unsplit", "ANY") # the default method
+}
+
+\keyword{methods}
diff --git a/man/xtabs.Rd b/man/xtabs.Rd
index 64352ee..0e50b05 100644
--- a/man/xtabs.Rd
+++ b/man/xtabs.Rd
@@ -51,9 +51,9 @@ 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 \pkg{IRanges} package
- for an example of a specific \code{xtabs} method (defined for
- \link[IRanges]{DataTable} objects).
+ \item \link[S4Vectors]{xtabs,DataTable-method} in the \pkg{S4Vectors}
+ package for an example of a specific \code{xtabs} method (defined
+ for \link[S4Vectors]{DataTable} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
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