[med-svn] [r-bioc-biocgenerics] 01/03: Imported Upstream version 0.22.0
Graham Inggs
ginggs at moszumanska.debian.org
Fri May 12 15:44:49 UTC 2017
This is an automated email from the git hooks/post-receive script.
ginggs pushed a commit to branch master
in repository r-bioc-biocgenerics.
commit 1922273abdce123b92fd94b0f708791d7f91a20b
Author: Graham Inggs <ginggs at debian.org>
Date: Fri May 12 16:15:38 2017 +0200
Imported Upstream version 0.22.0
---
DESCRIPTION | 20 +++++++--------
NAMESPACE | 13 ++++++++++
R/is.unsorted.R | 2 +-
R/matrix-summary.R | 8 ++++++
R/{rank.R => mean.R} | 5 ++--
R/rank.R | 17 ++++++++++++-
R/replaceSlots.R | 2 +-
R/{rank.R => t.R} | 5 ++--
R/{rank.R => var.R} | 7 ++++--
man/matrix-summary.Rd | 67 +++++++++++++++++++++++++++++++++++++++++++++++++++
man/mean.Rd | 64 ++++++++++++++++++++++++++++++++++++++++++++++++
man/order.Rd | 2 +-
man/rank.Rd | 9 ++++++-
man/sets.Rd | 13 +++++-----
man/t.Rd | 62 +++++++++++++++++++++++++++++++++++++++++++++++
man/var.Rd | 65 +++++++++++++++++++++++++++++++++++++++++++++++++
16 files changed, 332 insertions(+), 29 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 3d4c0a7..a37a626 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: BiocGenerics
Title: S4 generic functions for Bioconductor
Description: S4 generic functions needed by many Bioconductor packages.
-Version: 0.20.0
+Version: 0.22.0
Author: The Bioconductor Dev Team
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
biocViews: Infrastructure
@@ -14,13 +14,13 @@ License: Artistic-2.0
Collate: S3-classes-as-S4-classes.R normarg-utils.R replaceSlots.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 grep.R
- is.unsorted.R lapply.R lengths.R mapply.R match.R nrow.R
- order.R paste.R rank.R rep.R row_colnames.R sets.R sort.R
- start.R subset.R table.R tapply.R unique.R unlist.R unsplit.R
- relist.R which.R boxplot.R image.R density.R IQR.R mad.R
- residuals.R weights.R xtabs.R clusterApply.R annotation.R
- combine.R dbconn.R dge.R fileName.R normalize.R
- organism_species.R plotMA.R plotPCA.R score.R strand.R
- updateObject.R testPackage.R zzz.R
+ is.unsorted.R lapply.R lengths.R mapply.R match.R
+ matrix-summary.R mean.R nrow.R order.R paste.R rank.R rep.R
+ row_colnames.R sets.R sort.R start.R subset.R t.R table.R
+ tapply.R unique.R unlist.R unsplit.R relist.R var.R which.R
+ boxplot.R image.R density.R IQR.R mad.R residuals.R weights.R
+ xtabs.R clusterApply.R annotation.R combine.R dbconn.R dge.R
+ fileName.R normalize.R organism_species.R plotMA.R plotPCA.R
+ score.R strand.R updateObject.R testPackage.R zzz.R
NeedsCompilation: no
-Packaged: 2016-10-17 22:55:18 UTC; biocbuild
+Packaged: 2017-04-24 23:11:07 UTC; biocbuild
diff --git a/NAMESPACE b/NAMESPACE
index 0b07e2d..ac94259 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -75,6 +75,13 @@ export(
## from R/match.R:
match,
+ ## from R/matrix-summary.R:
+ rowSums, rowMeans,
+ colSums, colMeans,
+
+ ## from R/mean.R:
+ mean,
+
## from R/nrow.R:
nrow, ncol, NROW, NCOL,
@@ -107,6 +114,9 @@ export(
## from R/subset.R:
subset,
+ ## from R/t.R:
+ t,
+
## from R/table.R:
table,
@@ -155,6 +165,9 @@ export(
## from R/residuals.R:
residuals,
+ ## from R/var.R:
+ var, sd,
+
## from R/weights.R:
weights,
diff --git a/R/is.unsorted.R b/R/is.unsorted.R
index 0c60cbe..bff2cc3 100644
--- a/R/is.unsorted.R
+++ b/R/is.unsorted.R
@@ -7,7 +7,7 @@
### the 'ignore.strand' argument for the method for GenomicRanges objects).
.is.unsorted.useAsDefault <- function(x, na.rm=FALSE, strictly=FALSE, ...)
- base::is.unsorted(x, na.rm, strictly, ...)
+ base::is.unsorted(x, na.rm=na.rm, strictly=strictly, ...)
setGeneric("is.unsorted", signature="x",
function(x, na.rm=FALSE, strictly=FALSE, ...)
diff --git a/R/matrix-summary.R b/R/matrix-summary.R
new file mode 100644
index 0000000..f3bd4bd
--- /dev/null
+++ b/R/matrix-summary.R
@@ -0,0 +1,8 @@
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+### Row-level and column-level summary
+###
+
+setGeneric("rowSums", signature="x")
+setGeneric("colSums", signature="x")
+setGeneric("rowMeans", signature="x")
+setGeneric("colMeans", signature="x")
diff --git a/R/rank.R b/R/mean.R
similarity index 73%
copy from R/rank.R
copy to R/mean.R
index 4954af8..1fd70de 100644
--- a/R/rank.R
+++ b/R/mean.R
@@ -1,7 +1,6 @@
### =========================================================================
-### The rank() generic
+### The mean() generic
### -------------------------------------------------------------------------
###
-setGeneric("rank", signature="x")
-
+setGeneric("mean")
diff --git a/R/rank.R b/R/rank.R
index 4954af8..488f2af 100644
--- a/R/rank.R
+++ b/R/rank.R
@@ -3,5 +3,20 @@
### -------------------------------------------------------------------------
###
-setGeneric("rank", signature="x")
+### base::rank() doesn't have the ellipsis. We add it to the generic
+### function defined below so methods can support additional arguments (e.g.
+### the 'ignore.strand' argument for the method for GenomicRanges objects).
+
+.is.rank.useAsDefault <- function(x, na.last=TRUE,
+ ties.method=c("average", "first", "last", "random", "max", "min"), ...)
+{
+ base::rank(x, na.last=na.last, ties.method=ties.method, ...)
+}
+
+setGeneric("rank", signature="x",
+ function(x, na.last=TRUE,
+ ties.method=c("average", "first", "last", "random", "max", "min"), ...)
+ standardGeneric("rank"),
+ useAsDefault=.is.rank.useAsDefault
+)
diff --git a/R/replaceSlots.R b/R/replaceSlots.R
index b2ef4d5..d6d057c 100644
--- a/R/replaceSlots.R
+++ b/R/replaceSlots.R
@@ -45,7 +45,7 @@ unsafe_replaceSlots <- function(object, ..., .slotList=list())
if (first_time) {
## Triggers a copy.
slot(object, slot_name, check=FALSE) <- slot_val
- first_time <<- FALSE
+ first_time <- FALSE
} else {
## In-place modification (i.e. no copy).
`slot<-`(object, slot_name, check=FALSE, slot_val)
diff --git a/R/rank.R b/R/t.R
similarity index 73%
copy from R/rank.R
copy to R/t.R
index 4954af8..5569a98 100644
--- a/R/rank.R
+++ b/R/t.R
@@ -1,7 +1,6 @@
### =========================================================================
-### The rank() generic
+### The t() generic
### -------------------------------------------------------------------------
###
-setGeneric("rank", signature="x")
-
+setGeneric("t")
diff --git a/R/rank.R b/R/var.R
similarity index 51%
copy from R/rank.R
copy to R/var.R
index 4954af8..f825d9c 100644
--- a/R/rank.R
+++ b/R/var.R
@@ -1,7 +1,10 @@
### =========================================================================
-### The rank() generic
+### The var() and sd() generics
### -------------------------------------------------------------------------
###
+### Dispatches only on 'x' (and 'y' for var)
+###
-setGeneric("rank", signature="x")
+setGeneric("var", signature=c("x", "y"))
+setGeneric("sd", signature="x")
diff --git a/man/matrix-summary.Rd b/man/matrix-summary.Rd
new file mode 100644
index 0000000..5464e7e
--- /dev/null
+++ b/man/matrix-summary.Rd
@@ -0,0 +1,67 @@
+\name{matrix-summary}
+
+\alias{rowSums}
+\alias{colSums}
+\alias{rowMeans}
+\alias{colMeans}
+
+\title{Form Row and Column Sums and Means}
+
+\description{
+ Form row and column sums and means for rectangular objects..
+
+ NOTE: This man page is for the \code{rowSums}, \code{colSums},
+ \code{rowMeans}, and \code{colMeans} \emph{S4 generic functions}
+ defined in the \pkg{BiocGenerics} package.
+ See \code{?base::\link[base]{colSums}} for the default methods
+ (defined in the \pkg{base} package).
+ Bioconductor packages can define specific methods for objects
+ (typically array-like) not supported by the default method.
+}
+
+\usage{
+ colSums (x, na.rm = FALSE, dims = 1)
+ rowSums (x, na.rm = FALSE, dims = 1)
+ colMeans(x, na.rm = FALSE, dims = 1)
+ rowMeans(x, na.rm = FALSE, dims = 1)
+}
+
+\arguments{
+ \item{x}{
+ a rectangular object, like a matrix or data frame
+ }
+ \item{na.rm, dims}{see \link[base]{colSums}}
+}
+
+\value{
+ See \code{?base::\link[base]{colSums}} for the value returned by the
+ default methods.
+
+ Specific methods defined in Bioconductor packages will typically
+ return an object of the same class as the input object.
+}
+
+\seealso{
+ \itemize{
+ \item \code{base::\link[base]{colSums}} for the default
+ \code{colSums}, \code{rowSums}, \code{colMeans}, and \code{colSums}
+ methods.
+
+ \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{
+colSums
+showMethods("colSums")
+selectMethod("colSums", "ANY") # the default method
+}
+
+\keyword{methods}
diff --git a/man/mean.Rd b/man/mean.Rd
new file mode 100644
index 0000000..ba86629
--- /dev/null
+++ b/man/mean.Rd
@@ -0,0 +1,64 @@
+\name{mean}
+
+\alias{mean}
+
+\title{Arithmetic Mean}
+
+\description{
+ Generic function for the (trimmed) arithmetic mean.
+
+ NOTE: This man page is for the \code{mean} \emph{S4 generic function}
+ defined in the \pkg{BiocGenerics} package.
+ See \code{?base::\link[base]{mean}} for the default method
+ (defined in the \pkg{base} package).
+ Bioconductor packages can define specific methods for objects
+ (typically vector-like) not supported by the default method.
+}
+
+\usage{
+mean(x, ...)
+}
+
+\arguments{
+ \item{x}{
+ typically a vector-like object
+ }
+ \item{...}{
+ see \code{\link[base]{mean}}
+ }
+}
+
+\value{
+ See \code{?base::\link[base]{mean}} for the value returned by the
+ default method.
+
+ Specific methods defined in Bioconductor packages will typically
+ return an object of the same class as the input object.
+}
+
+\seealso{
+ \itemize{
+ \item \code{base::\link[base]{mean}} for the default \code{mean} 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[S4Vectors]{mean,Rle-method} in the \pkg{S4Vectors} package
+ for an example of a specific \code{mean} method (defined for
+ \link[S4Vectors]{Rle} objects).
+
+ \item \link{BiocGenerics} for a summary of all the generics defined
+ in the \pkg{BiocGenerics} package.
+ }
+}
+
+\examples{
+mean
+showMethods("mean")
+selectMethod("mean", "ANY") # the default method
+}
+
+\keyword{methods}
diff --git a/man/order.Rd b/man/order.Rd
index d931df4..28af540 100644
--- a/man/order.Rd
+++ b/man/order.Rd
@@ -18,7 +18,7 @@
}
\usage{
-order(..., na.last=TRUE, decreasing=FALSE, method=c("shell", "radix"))
+order(..., na.last=TRUE, decreasing=FALSE, method=c("auto", "shell", "radix"))
}
\arguments{
diff --git a/man/rank.Rd b/man/rank.Rd
index e20574a..e3fe5ff 100644
--- a/man/rank.Rd
+++ b/man/rank.Rd
@@ -18,7 +18,8 @@
\usage{
rank(x, na.last=TRUE,
- ties.method=c("average", "first", "last", "random", "max", "min"))
+ ties.method=c("average", "first", "last", "random", "max", "min"),
+ ...)
}
\arguments{
@@ -29,6 +30,12 @@ rank(x, na.last=TRUE,
See \code{?base::\link[base]{rank}} for a description of
these arguments.
}
+ \item{...}{
+ Additional arguments, for use in specific methods.
+
+ Note that \code{base::\link[base]{rank}} (the default method) only
+ takes the \code{x}, \code{na.last}, and \code{ties.method} arguments.
+ }
}
\value{
diff --git a/man/sets.Rd b/man/sets.Rd
index 50cf11a..eeb3c52 100644
--- a/man/sets.Rd
+++ b/man/sets.Rd
@@ -54,9 +54,9 @@ setdiff(x, y, ...)
binary operation, this typically allows methods to add extra arguments
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 \pkg{GenomicRanges} package). (Note that the \code{union} and
- \code{intersect} methods for those objects also support the
+ \code{setdiff} method for \link[GenomicRanges]{GenomicRanges} objects
+ (defined in the \pkg{GenomicRanges} package). (Note that the \code{union}
+ and \code{intersect} methods for those objects also support the
\code{ignore.strand} argument.)
}
@@ -71,9 +71,10 @@ setdiff(x, y, ...)
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
- \item \link[GenomicRanges]{union,GRanges,GRanges-method} in the
- \pkg{GenomicRanges} package for an example of a specific \code{union}
- method (defined for \link[GenomicRanges]{GRanges} objects).
+ \item \link[GenomicRanges]{union,GenomicRanges,GenomicRanges-method} in
+ the \pkg{GenomicRanges} package for examples of specific
+ \code{union}, \code{intersect}, and \code{setdiff} methods (defined
+ for \link[GenomicRanges]{GenomicRanges} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
diff --git a/man/t.Rd b/man/t.Rd
new file mode 100644
index 0000000..e5480bf
--- /dev/null
+++ b/man/t.Rd
@@ -0,0 +1,62 @@
+\name{t}
+
+\alias{t}
+
+\title{Matrix Transponse}
+
+\description{
+ Given a rectangular object \code{x}, \code{t} returns the
+ transpose of \code{x}.
+
+ NOTE: This man page is for the \code{t} \emph{S4 generic function}
+ defined in the \pkg{BiocGenerics} package.
+ See \code{?base::\link[base]{t}} for the default method
+ (defined in the \pkg{base} package).
+ Bioconductor packages can define specific methods for objects
+ (typically array-like) not supported by the default method.
+}
+
+\usage{
+t(x)
+}
+
+\arguments{
+ \item{x}{
+ a rectangular object, like a matrix or data frame
+ }
+}
+
+\value{
+ See \code{?base::\link[base]{t}} for the value returned by the
+ default method.
+
+ Specific methods defined in Bioconductor packages will typically
+ return an object of the same class as the input object.
+}
+
+\seealso{
+ \itemize{
+ \item \code{base::\link[base]{t}} for the default \code{t} 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[S4Vectors]{t,Hits-method} in the \pkg{S4Vectors} package
+ for an example of a specific \code{t} method (defined for
+ \link[S4Vectors]{Hits} objects).
+
+ \item \link{BiocGenerics} for a summary of all the generics defined
+ in the \pkg{BiocGenerics} package.
+ }
+}
+
+\examples{
+t
+showMethods("t")
+selectMethod("t", "ANY") # the default method
+}
+
+\keyword{methods}
diff --git a/man/var.Rd b/man/var.Rd
new file mode 100644
index 0000000..a942f0e
--- /dev/null
+++ b/man/var.Rd
@@ -0,0 +1,65 @@
+\name{var}
+
+\alias{var}
+\alias{sd}
+
+\title{Variance and Standard Deviation}
+
+\description{
+ \code{var} and \code{sd} compute the variance and standard deviation
+ of a vector \code{x}.
+
+ NOTE: This man page is for the \code{var} and \code{sd},
+ \emph{S4 generic functions} defined in the \pkg{BiocGenerics} package.
+ See \code{?stats::\link[stats]{var}} and \code{?stats::\link[stats]{sd}}
+ for the default methods (defined in the \pkg{stats} package).
+ Bioconductor packages can define specific methods for objects
+ (typically array-like) not supported by the default method.
+}
+
+\usage{
+ var(x, y = NULL, na.rm = FALSE, use)
+ sd(x, na.rm = FALSE)
+}
+
+\arguments{
+ \item{x}{
+ a vector-like object
+ }
+ \item{y}{
+ a vector-like object, or \code{NULL}
+ }
+ \item{na.rm, use}{see \link[stats]{var}}
+}
+
+\value{
+ See \code{?stats::\link[stats]{var}} and \code{?stats::\link[stats]{sd}}
+ for the value returned by the default methods.
+
+ Specific methods defined in Bioconductor packages will typically
+ return an object of the same class as the input object.
+}
+
+\seealso{
+ \itemize{
+ \item \code{stats::\link[stats]{var}} and \code{stats::\link[stats]{sd}}
+ for the default methods.
+
+ \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{
+var
+showMethods("var")
+selectMethod("var", "ANY") # the default method
+}
+
+\keyword{methods}
--
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