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commit 1922273abdce123b92fd94b0f708791d7f91a20b Author: Graham Inggs <[email protected]> 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 <[email protected]> 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} -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-biocgenerics.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
