[med-svn] [r-bioc-biocgenerics] 01/04: Imported Upstream version 0.14.0
Andreas Tille
tille at debian.org
Sat May 9 05:39:05 UTC 2015
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 1de16c4116a27e287cc5254795940ff78841d7c3
Author: Andreas Tille <tille at debian.org>
Date: Sat May 9 07:27:52 2015 +0200
Imported Upstream version 0.14.0
---
DESCRIPTION | 27 +++++-----
NAMESPACE | 26 ++++++++--
R/S3-classes-as-S4-classes.R | 2 +
R/fileName.R | 6 +++
R/normarg-utils.R | 10 ++++
R/organism_species.R | 16 ++++++
R/plotPCA.R | 3 ++
R/score.R | 10 ++++
R/show-utils.R | 81 ++++++++++++++++++++++--------
R/testPackage.R | 14 +++---
R/{update.R => update-utils.R} | 8 ++-
inst/CITATION | 14 ++++++
man/BiocGenerics-package.Rd | 13 +++++
man/S3-classes-as-S4-classes.Rd | 5 +-
man/fileName.Rd | 51 +++++++++++++++++++
man/organism_species.Rd | 108 ++++++++++++++++++++++++++++++++++++++++
man/plotPCA.Rd | 56 +++++++++++++++++++++
man/rank.Rd | 4 +-
man/score.Rd | 63 +++++++++++++++++++++++
man/strand.Rd | 6 +++
20 files changed, 473 insertions(+), 50 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 290cafb..07c1d61 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,22 +1,25 @@
Package: BiocGenerics
Title: S4 generic functions for Bioconductor
Description: S4 generic functions needed by many Bioconductor packages.
-Version: 0.12.0
+Version: 0.14.0
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, S4Vectors, IRanges, GenomicRanges, AnnotationDbi,
- oligoClasses, oligo, affyPLM, flowClust, affy, RUnit, DESeq2
+ oligoClasses, oligo, affyPLM, flowClust, affy, DESeq2, MSnbase,
+ annotate, RUnit
License: Artistic-2.0
-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
- 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
+Collate: S3-classes-as-S4-classes.R normarg-utils.R update-utils.R
+ show-utils.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 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 fileName.R normalize.R
+ organism_species.R plotMA.R plotPCA.R score.R strand.R
+ updateObject.R testPackage.R test_BiocGenerics_package.R zzz.R
+NeedsCompilation: no
+Packaged: 2015-04-17 03:42:27 UTC; biocbuild
diff --git a/NAMESPACE b/NAMESPACE
index b5f2522..f52baab 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,8 +11,9 @@ exportClasses(
fifo, sockconn, terminal, textConnection,
gzcon,
characterORconnection,
- AsIs
- #table, xtabs
+ AsIs,
+ #table, xtabs,
+ dist
)
@@ -165,9 +166,25 @@ export(
## from R/combine.R:
combine,
+ ## from R/fileName.R:
+ fileName,
+
## from R/normalize.R:
normalize,
+ ## from R/organism_species.R:
+ organism, "organism<-",
+ species, "species<-",
+
+ ## from R/plotMA.R:
+ plotMA,
+
+ ## from R/plotPCA.R:
+ plotPCA,
+
+ ## from R/score.R:
+ score, "score<-",
+
## from R/strand.R:
strand, "strand<-",
@@ -192,8 +209,9 @@ exportMethods(
conditions, "conditions<-",
estimateSizeFactors,
estimateDispersions,
- plotDispEsts,
- plotMA
+ plotDispEsts,
+ plotMA,
+ plotPCA
)
diff --git a/R/S3-classes-as-S4-classes.R b/R/S3-classes-as-S4-classes.R
index ea1a60b..8b765a3 100644
--- a/R/S3-classes-as-S4-classes.R
+++ b/R/S3-classes-as-S4-classes.R
@@ -24,3 +24,5 @@ setOldClass("AsIs")
# Warning: replacing previous import
# ‘.__C__table’ when loading ‘BiocGenerics’
+setOldClass("dist")
+
diff --git a/R/fileName.R b/R/fileName.R
new file mode 100644
index 0000000..e8f15d1
--- /dev/null
+++ b/R/fileName.R
@@ -0,0 +1,6 @@
+### =========================================================================
+### The fileName() generic
+### -------------------------------------------------------------------------
+
+setGeneric("fileName", function(object, ...) standardGeneric("fileName"))
+
diff --git a/R/normarg-utils.R b/R/normarg-utils.R
index 2bbe02b..5b6636a 100644
--- a/R/normarg-utils.R
+++ b/R/normarg-utils.R
@@ -2,6 +2,16 @@
### Utility functions for checking/fixing user-supplied arguments
### -------------------------------------------------------------------------
+### NOTE: The stuff in this file (not exported) is a copy/paste of some of
+### the functions in S4Vectors but it doesn't really belong to BiocGenerics.
+### It seems that the only reason for having it duplicated here is that it's
+### used by the stuff in the update-utils.R file. However the stuff in
+### update-utils.R doesn't really belong to BiocGenerics either!
+###
+### TODO: This stuff would need to be moved to a more appropriate place (when
+### we have one), and then we should get rid of the duplication between the
+### functions below and the same functions in S4Vectors.
+
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### For checking only.
###
diff --git a/R/organism_species.R b/R/organism_species.R
new file mode 100644
index 0000000..bdd3cd7
--- /dev/null
+++ b/R/organism_species.R
@@ -0,0 +1,16 @@
+### =========================================================================
+### The organism(), `organism<-`(), species(), and `species<-`() generics
+### -------------------------------------------------------------------------
+
+setGeneric("organism", function(object) standardGeneric("organism"))
+
+setGeneric("organism<-", signature="object",
+ function(object, value) standardGeneric("organism<-")
+)
+
+setGeneric("species", function(object) standardGeneric("species"))
+
+setGeneric("species<-", signature="object",
+ function(object, value) standardGeneric("species<-")
+)
+
diff --git a/R/plotPCA.R b/R/plotPCA.R
new file mode 100644
index 0000000..bfaeac0
--- /dev/null
+++ b/R/plotPCA.R
@@ -0,0 +1,3 @@
+setGeneric("plotPCA", function(object, ...) {
+ standardGeneric("plotPCA")
+})
diff --git a/R/score.R b/R/score.R
new file mode 100644
index 0000000..ce4b8fb
--- /dev/null
+++ b/R/score.R
@@ -0,0 +1,10 @@
+### =========================================================================
+### The score() and `score<-`() generics
+### -------------------------------------------------------------------------
+
+setGeneric("score", function(x, ...) standardGeneric("score"))
+
+setGeneric("score<-", signature="x",
+ function(x, ..., value) standardGeneric("score<-")
+)
+
diff --git a/R/show-utils.R b/R/show-utils.R
index 58e713f..37e8407 100644
--- a/R/show-utils.R
+++ b/R/show-utils.R
@@ -4,27 +4,40 @@
###
labeledLine <-
- function(label, els, count = TRUE, labelSep = ":", sep = " ", ellipsis = "...")
+ function(label, els, count = TRUE, labelSep = ":", sep = " ", ellipsis = "...",
+ ellipsisPos = c("middle", "end", "start"))
{
if (count && !is.null(els))
label <- paste(label, "(", length(els), ")", sep = "")
label <- paste(label, labelSep, sep, sep = "")
width <- getOption("width") - nchar(label)
- line <- ellipsize(els, width, sep, ellipsis)
+ line <- ellipsize(els, width, sep, ellipsis, ellipsisPos)
paste(label, line, "\n", sep = "")
}
ellipsize <-
- function(obj, width = getOption("width"), sep = " ", ellipsis = "...")
+ function(obj, width = getOption("width"), sep = " ", ellipsis = "...",
+ pos = c("middle", "end", "start"))
{
+ pos <- match.arg(pos)
if (is.null(obj))
obj <- "NULL"
- if (length(obj) > 2 * width)
- obj <- c(head(obj, width), tail(obj, width))
- str <- encodeString(obj)
+ if (is.factor(obj))
+ obj <- as.character(obj)
## get order selectSome() would print
- half <- seq_len(ceiling(length(obj) / 2))
- ind <- as.vector(rbind(half, length(obj) - half + 1))
+ if (pos == "middle") {
+ if (length(obj) > 2 * width)
+ obj <- c(head(obj, width), tail(obj, width))
+ half <- seq_len(ceiling(length(obj) / 2L))
+ ind <- as.vector(rbind(half, length(obj) - half + 1L))
+ } else if (pos == "end") {
+ obj <- head(obj, width)
+ ind <- seq_len(length(obj))
+ } else {
+ obj <- tail(obj, width)
+ ind <- rev(seq_len(length(obj)))
+ }
+ str <- encodeString(obj)
nc <- cumsum(nchar(str[ind]) + nchar(sep)) - nchar(sep)
last <- findInterval(width, nc)
if (length(obj) > last) {
@@ -32,30 +45,54 @@ ellipsize <-
while (last &&
(nc[last] + nchar(sep)*2^(last>1) + nchar(ellipsis)) > width)
last <- last - 1L
- if (last == 0) ## have to truncate the first element
- str <-
- paste(substring(str[1L], 1, width - nchar(ellipsis)), ellipsis,
- sep = "")
- else if (last == 1) ## can only show the first
- str <- c(str[1L], "...")
- else
- str <- selectSome(str, last + 1L)
+ if (last == 0) { ## have to truncate the first/last element
+ if (pos == "start") {
+ str <-
+ paste(ellipsis,
+ substring(tail(str, 1L),
+ nchar(tail(str, 1L))-(width-nchar(ellipsis))+1L,
+ nchar(ellipsis)),
+ sep = "")
+ } else {
+ str <-
+ paste(substring(str[1L], 1, width - nchar(ellipsis)), ellipsis,
+ sep = "")
+ }
+ }
+ else if (last == 1) { ## can only show the first/last
+ if (pos == "start")
+ str <- c(ellipsis, tail(str, 1L))
+ else str <- c(str[1L], ellipsis)
+ }
+ else {
+ str <- selectSome(str, last + 1L, ellipsis, pos)
+ }
}
paste(str, collapse = sep)
}
-## taken directly from Biobase
-selectSome <- function(obj, maxToShow = 5)
+## taken directly from Biobase, then added 'ellipsisPos' argument
+selectSome <- function(obj, maxToShow = 5, ellipsis = "...",
+ ellipsisPos = c("middle", "end", "start"), quote=FALSE)
{
+ if(is.character(obj) && quote)
+ obj <- sQuote(obj)
+ ellipsisPos <- match.arg(ellipsisPos)
len <- length(obj)
if (maxToShow < 3)
maxToShow <- 3
if (len > maxToShow) {
maxToShow <- maxToShow - 1
- bot <- ceiling(maxToShow/2)
- top <- len - (maxToShow - bot - 1)
- nms <- obj[c(1:bot, top:len)]
- c(as.character(nms[1:bot]), "...", as.character(nms[-c(1:bot)]))
+ if (ellipsisPos == "end") {
+ c(head(obj, maxToShow), ellipsis)
+ } else if (ellipsisPos == "start") {
+ c(ellipsis, tail(obj, maxToShow))
+ } else {
+ bot <- ceiling(maxToShow/2)
+ top <- len - (maxToShow - bot - 1)
+ nms <- obj[c(1:bot, top:len)]
+ c(as.character(nms[1:bot]), ellipsis, as.character(nms[-c(1:bot)]))
+ }
} else {
obj
}
diff --git a/R/testPackage.R b/R/testPackage.R
index 8c63151..460870d 100644
--- a/R/testPackage.R
+++ b/R/testPackage.R
@@ -25,14 +25,14 @@ testPackage <- function(pkgname, subdir="unitTests", pattern="^test_.*\\.R$")
RUnit_opts$silent <- TRUE
RUnit_opts$verbose_fail_msg <- TRUE
options(RUnit = RUnit_opts)
- suite <- defineTestSuite(name=paste(pkgname, "RUnit Tests"),
- dirs=dir,
- testFileRegexp=pattern,
- rngKind="default",
- rngNormalKind="default")
- result <- runTestSuite(suite)
+ suite <- RUnit::defineTestSuite(name=paste(pkgname, "RUnit Tests"),
+ dirs=dir,
+ testFileRegexp=pattern,
+ rngKind="default",
+ rngNormalKind="default")
+ result <- RUnit::runTestSuite(suite)
cat("\n\n")
- printTextProtocol(result, showDetails=FALSE)
+ RUnit::printTextProtocol(result, showDetails=FALSE)
if (length(details <- .failure_details(result)) >0) {
cat("\nTest files with failing tests\n")
for (i in seq_along(details)) {
diff --git a/R/update.R b/R/update-utils.R
similarity index 86%
rename from R/update.R
rename to R/update-utils.R
index f3f84f2..40fda6b 100644
--- a/R/update.R
+++ b/R/update-utils.R
@@ -2,7 +2,11 @@
### Efficient update behavior for S4 objects
### -------------------------------------------------------------------------
###
-### 'updateS4' is essentially a more efficient initialize for (value) S4 objects.
+### NOTE: The stuff in this file (not exported) doesn't really belong to
+### BiocGenerics.
+###
+### TODO: This stuff would need to be moved to a more appropriate place (when
+### we have one).
unsafe_updateS4 <- function(object, ..., .slotList = list()) {
valid_argnames <- slotNames(object)
@@ -30,6 +34,8 @@ unsafe_updateS4 <- function(object, ..., .slotList = list()) {
listUpdate(listUpdate(object, args), .slotList)
}
+### 'updateS4' is essentially a more efficient initialize for (value) S4
+### objects.
updateS4 <- function(object, ..., check = TRUE) {
if (!isTRUEorFALSE(check))
stop("'check' must be TRUE or FALSE")
diff --git a/inst/CITATION b/inst/CITATION
new file mode 100644
index 0000000..1c2f680
--- /dev/null
+++ b/inst/CITATION
@@ -0,0 +1,14 @@
+citEntry(entry="Article",
+ author = "Huber, W. and Carey, V. J. and Gentleman, R. and Anders, S. and Carlson, M. and Carvalho, B. S. and Bravo, H. C. and Davis, S. and Gatto, L. and Girke, T. and Gottardo, R. and Hahne, F. and Hansen, K. D. and Irizarry, R. A. and Lawrence, M. and Love, M. I. and MacDonald, J. and Obenchain, V. and {Ole\'s}, A. K. and {Pag\`es}, H. and Reyes, A. and Shannon, P. and Smyth, G. K. and Tenenbaum, D. and Waldron, L. and Morgan, M. ",
+ title = "{O}rchestrating high-throughput genomic analysis with {B}ioconductor",
+ journal = "Nature Methods",
+ year = "2015",
+ volume = "12",
+ number = "2",
+ pages = "115--121",
+ url = "http://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3252.html",
+ textVersion = paste(
+ "Orchestrating high-throughput genomic analysis with Bioconductor.",
+ "W. Huber, V.J. Carey, R. Gentleman, ..., M. Morgan",
+ "Nature Methods, 2015:12, 115.")
+)
diff --git a/man/BiocGenerics-package.Rd b/man/BiocGenerics-package.Rd
index c887bc3..aacf8f6 100644
--- a/man/BiocGenerics-package.Rd
+++ b/man/BiocGenerics-package.Rd
@@ -152,8 +152,21 @@
\item \code{\link[BiocGenerics]{combine}}
+ \item \code{\link[BiocGenerics]{fileName}}
+
\item \code{\link[BiocGenerics]{normalize}}
+ \item \code{\link[BiocGenerics]{organism}},
+ \code{\link[BiocGenerics]{organism<-}},
+ \code{\link[BiocGenerics]{species}},
+ \code{\link[BiocGenerics]{species<-}}
+
+ \item \code{\link[BiocGenerics]{plotMA}}
+ \item \code{\link[BiocGenerics]{plotPCA}}
+
+ \item \code{\link[BiocGenerics]{score}},
+ \code{\link[BiocGenerics]{score<-}}
+
\item \code{\link[BiocGenerics]{strand}},
\code{\link[BiocGenerics]{strand<-}}
diff --git a/man/S3-classes-as-S4-classes.Rd b/man/S3-classes-as-S4-classes.Rd
index e608a05..48bfc2c 100644
--- a/man/S3-classes-as-S4-classes.Rd
+++ b/man/S3-classes-as-S4-classes.Rd
@@ -19,6 +19,7 @@
\alias{AsIs-class}
%\alias{table-class}
%\alias{xtabs-class}
+\alias{dist-class}
\title{S3 classes as S4 classes}
@@ -33,14 +34,14 @@
S3 classes currently turned into S4 classes:
\itemize{
\item connection class and subclasses:
- connection,
+ \link{connection},
file, url, gzfile, bzfile, unz, pipe,
fifo, sockconn, terminal, textConnection,
gzcon.
Addtitionally the characterORconnection S4 class is defined as
the union of classes character and connection.
- \item others: AsIs
+ \item others: \link{AsIs}, \link{dist}
}
}
diff --git a/man/fileName.Rd b/man/fileName.Rd
new file mode 100644
index 0000000..a0abb50
--- /dev/null
+++ b/man/fileName.Rd
@@ -0,0 +1,51 @@
+\name{fileName}
+
+\alias{fileName}
+
+\title{Accessing the file name of an object}
+
+\description{
+ Get the file name of an object.
+}
+
+\usage{
+fileName(object, ...)
+}
+
+\arguments{
+ \item{object}{
+ An object with a file name.
+ }
+ \item{...}{
+ Additional arguments, for use in specific methods.
+ }
+}
+
+\seealso{
+ \itemize{
+ \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[MSnbase]{fileName,MSmap-method} in the
+ \pkg{MSnbase} package for an example of a specific
+ \code{fileName} method (defined for \link[MSnbase]{MSmap}
+ objects).
+
+ \item \link{BiocGenerics} for a summary of all the generics defined
+ in the \pkg{BiocGenerics} package.
+ }
+}
+
+\examples{
+fileName
+showMethods("fileName")
+
+library(MSnbase)
+showMethods("fileName")
+selectMethod("fileName", "MSmap")
+}
+
+\keyword{methods}
diff --git a/man/organism_species.Rd b/man/organism_species.Rd
new file mode 100644
index 0000000..fd2f636
--- /dev/null
+++ b/man/organism_species.Rd
@@ -0,0 +1,108 @@
+\name{organism_species}
+
+\alias{organism_species}
+\alias{organism}
+\alias{organism<-}
+\alias{species}
+\alias{species<-}
+
+\title{Organism and species accessors}
+
+\description{
+ Get or set the organism and/or species of an object.
+}
+
+\usage{
+organism(object)
+organism(object) <- value
+
+species(object)
+species(object) <- value
+}
+
+\arguments{
+ \item{object}{
+ An object to get or set the organism or species of.
+ }
+ \item{value}{
+ The organism or species to set on \code{object}.
+ }
+}
+
+\value{
+ \code{organism} should return the \emph{scientific name} (i.e. genus and
+ species, or genus and species and subspecies) of the organism. Preferably
+ in the format \code{"Genus species"} (e.g. \code{"Homo sapiens"})
+ or \code{"Genus species subspecies"} (e.g.
+ \code{"Homo sapiens neanderthalensis"}).
+
+ \code{species} should of course return the species of the organism.
+ Unfortunately there is a long history of misuse of this accessor in
+ Bioconductor so its usage is now discouraged (starting with BioC 3.1).
+}
+
+\note{
+ TO DEVELOPPERS:
+
+ \code{species} has been historically misused in many places in Bioconductor
+ and is redundant with \code{organism}. So implementing the \code{species}
+ accessor is now discouraged (starting with BioC 3.1). The \code{organism}
+ accessor (returning the \emph{scientific name}) should be implemented
+ instead.
+}
+
+\seealso{
+ \itemize{
+ \item \url{http://bioconductor.org/packages/release/BiocViews.html#___Organism}
+ for browsing the annotation packages currently available in
+ Bioconductor by organism.
+
+ \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[annotate]{organism,character-method} and
+ \link[annotate]{organism,chromLocation-method} in the
+ \pkg{annotate} package for examples of specific \code{organism}
+ methods (defined for character and \link[annotate]{chromLocation}
+ objects).
+
+ \item \link[AnnotationDbi]{species,AnnotationDb-method} in the
+ \pkg{AnnotationDbi} package for an example of a specific
+ \code{species} method (defined for \link[AnnotationDbi]{AnnotationDb}
+ objects).
+
+ \item \link{BiocGenerics} for a summary of all the generics defined
+ in the \pkg{BiocGenerics} package.
+ }
+}
+
+\examples{
+## organism getter:
+organism
+showMethods("organism")
+
+library(annotate)
+showMethods("organism")
+selectMethod("organism", "character")
+selectMethod("organism", "chromLocation")
+
+## organism setter:
+`organism<-`
+showMethods("organism<-")
+
+## species getter:
+species
+showMethods("species")
+
+library(AnnotationDbi)
+selectMethod("species", "AnnotationDb")
+
+## species setter:
+`species<-`
+showMethods("species<-")
+}
+
+\keyword{methods}
diff --git a/man/plotPCA.Rd b/man/plotPCA.Rd
new file mode 100644
index 0000000..f3f1a32
--- /dev/null
+++ b/man/plotPCA.Rd
@@ -0,0 +1,56 @@
+\name{plotPCA}
+
+\alias{plotPCA}
+\alias{plotPCA,ANY-method}
+
+\title{PCA-plot: Principal Component Analysis plot}
+
+\description{
+ A generic function which produces a PCA-plot.
+}
+
+\usage{
+plotPCA(object, ...)
+}
+
+\arguments{
+ \item{object}{
+
+ A data object, typically containing gene expression information.
+
+ }
+ \item{...}{
+ Additional arguments, for use in specific methods.
+ }
+}
+
+\value{
+ Undefined. The function exists for its side effect, producing a plot.
+}
+
+\seealso{
+ \itemize{
+ \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 \code{\link[DESeq2]{plotPCA}} in the \pkg{DESeq2} package
+ for an example method that uses this generic.
+
+ \item \code{\link{BiocGenerics}} for a summary of all the generics defined
+ in the \pkg{BiocGenerics} package.
+ }
+}
+
+\examples{
+showMethods("plotPCA")
+
+suppressWarnings(
+ if(require("DESeq2"))
+ example("plotPCA", package="DESeq2", local=TRUE)
+)
+}
+
+\keyword{methods}
diff --git a/man/rank.Rd b/man/rank.Rd
index 465e2be..04d003b 100644
--- a/man/rank.Rd
+++ b/man/rank.Rd
@@ -63,9 +63,9 @@ 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 \pkg{IRanges} package
+ \item \link[S4Vectors]{rank,Vector-method} in the \pkg{S4Vectors} package
for an example of a specific \code{rank} method (defined for
- \link[IRanges]{Ranges} 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/score.Rd b/man/score.Rd
new file mode 100644
index 0000000..06db743
--- /dev/null
+++ b/man/score.Rd
@@ -0,0 +1,63 @@
+\name{score}
+
+\alias{score}
+\alias{score<-}
+
+\title{Score accessor}
+
+\description{
+ Get or set the score value contained in an object.
+}
+
+\usage{
+score(x, ...)
+score(x, ...) <- value
+}
+
+\arguments{
+ \item{x}{
+ An object to get or set the score value of.
+ }
+ \item{...}{
+ Additional arguments, for use in specific methods.
+ }
+ \item{value}{
+ The score value to set on \code{x}.
+ }
+}
+
+\seealso{
+ \itemize{
+ \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[GenomicRanges]{score,GenomicRanges-method} in the
+ \pkg{GenomicRanges} package for an example of a specific
+ \code{score} method (defined for \link[GenomicRanges]{GenomicRanges}
+ objects).
+
+ \item \link{BiocGenerics} for a summary of all the generics defined
+ in the \pkg{BiocGenerics} package.
+ }
+}
+
+\examples{
+score
+showMethods("score")
+
+`score<-`
+showMethods("score<-")
+
+library(GenomicRanges)
+
+showMethods("score")
+selectMethod("score", "GenomicRanges")
+
+showMethods("score<-")
+selectMethod("score<-", "GenomicRanges")
+}
+
+\keyword{methods}
diff --git a/man/strand.Rd b/man/strand.Rd
index a900899..937bf06 100644
--- a/man/strand.Rd
+++ b/man/strand.Rd
@@ -68,10 +68,16 @@ unstrand(x)
strand
showMethods("strand")
+`strand<-`
+showMethods("strand<-")
+
library(GenomicRanges)
+
showMethods("strand")
selectMethod("strand", "missing")
strand()
+
+showMethods("strand<-")
}
\keyword{methods}
--
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