@@ -15,20 +15,13 @@ export(colIQRs)

 export(colLogSumExps)

 export(colMadDiffs)

 export(colMads)

-export(colMaxs)

-export(colMeans2)

-export(colMedians)

-export(colMins)

 export(colOrderStats)

 export(colProds)

 export(colQuantiles)

-export(colRanges)

 export(colRanks)

 export(colSdDiffs)

-export(colSds)

 export(colTabulates)

 export(colVarDiffs)

-export(colVars)

 export(colWeightedMads)

 export(colWeightedMeans)

 export(colWeightedMedians)

@@ -49,21 +42,13 @@ export(rowIQRs)

 export(rowLogSumExps)

 export(rowMadDiffs)

 export(rowMads)

-export(rowMaxs)

-export(rowMeans2)

-export(rowMedians)

-export(rowMins)

 export(rowOrderStats)

 export(rowProds)

 export(rowQuantiles)

-export(rowRanges)

 export(rowRanks)

 export(rowSdDiffs)

-export(rowSds)

-export(rowSums2)

 export(rowTabulates)

 export(rowVarDiffs)

-export(rowVars)

 export(rowWeightedMads)

 export(rowWeightedMeans)

 export(rowWeightedMedians)

@@ -2,9 +2,7 @@

 # Sum

-

 #' @inherit MatrixGenerics::colSums2

-#'

 #' @export

 setMethod("colSums2", signature(x = "dgCMatrix"),

           function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

@@ -18,65 +16,68 @@ setMethod("colSums2", signature(x = "dgCMatrix"),

 })

-

 # Mean

-#' @inherit matrixStats::colMeans2

-#' @export

-setGeneric("colMeans2", function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-  matrixStats::colMeans2(as.matrix(x), rows = rows, cols = cols, na.rm = na.rm, ...)

-})

-

-

-#' @rdname colMeans2

+#' @inherit MatrixGenerics::colMeans2

 #' @export

 setMethod("colMeans2", signature(x = "dgCMatrix"),

-          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...)

-            dgCMatrix_colMeans2(x, na_rm = na.rm))

+          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

+  if(! is.null(rows)){

+    x <- x[rows, , drop = FALSE]

+  }

+  if(! is.null(cols)){

+    x <- x[, cols, drop = FALSE]

+  }

+  dgCMatrix_colMeans2(x, na_rm = na.rm)

+})

 # Median

-#' @inherit matrixStats::colMedians

+#' @inherit MatrixGenerics::colMedians

 #' @export

-setGeneric("colMedians", function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-  matrixStats::colMedians(as.matrix(x), rows = rows, cols = cols, na.rm = na.rm, ...)

+setMethod("colMedians", signature(x = "dgCMatrix"),

+          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

+  if(! is.null(rows)){

+    x <- x[rows, , drop = FALSE]

+  }

+  if(! is.null(cols)){

+    x <- x[, cols, drop = FALSE]

+  }

+  dgCMatrix_colMedians(x, na_rm = na.rm)

 })

-#' @rdname colMedians

-#' @export

-setMethod("colMedians", signature(x = "dgCMatrix"),

-          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...)

-            dgCMatrix_colMedians(x, na_rm = na.rm))

 # Vars

-#' @inherit matrixStats::colVars

-#' @export

-setGeneric("colVars", function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-  matrixStats::colVars(as.matrix(x), rows = rows, cols = cols, na.rm = na.rm, ...)

-})

-

-#' @rdname colVars

+#' @inherit MatrixGenerics::colVars

 #' @export

 setMethod("colVars", signature(x = "dgCMatrix"),

-          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...)

-            dgCMatrix_colVars(x, na_rm = na.rm))

+          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

+  if(! is.null(rows)){

+    x <- x[rows, , drop = FALSE]

+  }

+  if(! is.null(cols)){

+    x <- x[, cols, drop = FALSE]

+  }

+  dgCMatrix_colVars(x, na_rm = na.rm)

+})

 # Sds

-#' @inherit matrixStats::colSds

-#' @export

-setGeneric("colSds", function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-  matrixStats::colSds(as.matrix(x), rows = rows, cols = cols, na.rm = na.rm, ...)

-})

-

-#' @rdname colSds

+#' @inherit MatrixGenerics::colSds

 #' @export

 setMethod("colSds", signature(x = "dgCMatrix"),

-          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...)

-            sqrt(dgCMatrix_colVars(x, na_rm = na.rm)))

+          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

+  if(! is.null(rows)){

+    x <- x[rows, , drop = FALSE]

+  }

+  if(! is.null(cols)){

+    x <- x[, cols, drop = FALSE]

+  }

+  sqrt(dgCMatrix_colVars(x, na_rm = na.rm))

+})

 # Mads

@@ -139,32 +140,34 @@ setMethod("colProds", signature(x = "dgCMatrix"),

 # Min

-#' @inherit matrixStats::colMins

-#' @export

-setGeneric("colMins", function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-  matrixStats::colMins(as.matrix(x), rows = rows, cols = cols, na.rm = na.rm, ...)

-})

-

-#' @rdname colMins

+#' @inherit MatrixGenerics::colMins

 #' @export

 setMethod("colMins", signature(x = "dgCMatrix"),

-          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...)

-            dgCMatrix_colMins(x, na_rm = na.rm))

+          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

+  if(! is.null(rows)){

+    x <- x[rows, , drop = FALSE]

+  }

+  if(! is.null(cols)){

+    x <- x[, cols, drop = FALSE]

+  }

+  dgCMatrix_colMins(x, na_rm = na.rm)

+})

 # Max

-#' @inherit matrixStats::colMaxs

-#' @export

-setGeneric("colMaxs", function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-  matrixStats::colMaxs(as.matrix(x), rows = rows, cols = cols, na.rm = na.rm, ...)

-})

-

-#' @rdname colMaxs

+#' @inherit MatrixGenerics::colMaxs

 #' @export

 setMethod("colMaxs", signature(x = "dgCMatrix"),

-          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...)

-            dgCMatrix_colMaxs(x, na_rm = na.rm))

+          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

+  if(! is.null(rows)){

+    x <- x[rows, , drop = FALSE]

+  }

+  if(! is.null(cols)){

+    x <- x[, cols, drop = FALSE]

+  }

+  dgCMatrix_colMaxs(x, na_rm = na.rm)

+})

 # OrderStats

@@ -496,20 +499,20 @@ setMethod("colIQRs", signature(x = "dgCMatrix"),

 # colRanges

-#' @inherit matrixStats::colRanges

-#' @export

-setGeneric("colRanges", function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-  matrixStats::colRanges(as.matrix(x), rows = rows, cols = cols, na.rm = na.rm, ...)

-})

-

-#' @rdname colRanges

+#' @inherit MatrixGenerics::colRanges

 #' @export

 setMethod("colRanges", signature(x = "dgCMatrix"),

           function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-            col_max <- colMaxs(x, rows, cols, na.rm = na.rm)

-            col_min <- colMins(x, rows, cols, na.rm = na.rm)

-            unname(cbind(col_min, col_max))

-          })

+  if(! is.null(rows)){

+    x <- x[rows, , drop = FALSE]

+  }

+  if(! is.null(cols)){

+    x <- x[, cols, drop = FALSE]

+  }

+  col_max <- colMaxs(x, rows, cols, na.rm = na.rm)

+  col_min <- colMins(x, rows, cols, na.rm = na.rm)

+  unname(cbind(col_min, col_max))

+})

@@ -2,77 +2,83 @@

 # Sum

-#' @rdname colSums2

-#' @export

-setGeneric("rowSums2", function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-  matrixStats::rowSums2(as.matrix(x), rows = rows, cols = cols, na.rm = na.rm, ...)

-})

-

-#' @rdname colSums2

+#' @rdname colSums2-dgCMatrix-method

 #' @export

 setMethod("rowSums2", signature(x = "dgCMatrix"),

-          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...)

-            dgCMatrix_colSums2(t(x), na_rm = na.rm))

+          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

+  if(! is.null(rows)){

+    x <- x[rows, , drop = FALSE]

+  }

+  if(! is.null(cols)){

+    x <- x[, cols, drop = FALSE]

+  }

+  dgCMatrix_colSums2(t(x), na_rm = na.rm)

+})

 # Mean

-#' @rdname colMeans2

-#' @export

-setGeneric("rowMeans2", function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-  matrixStats::rowMeans2(as.matrix(x), rows = rows, cols = cols, na.rm = na.rm, ...)

-})

-

-#' @rdname colMeans2

+#' @rdname colMeans2-dgCMatrix-method

 #' @export

 setMethod("rowMeans2", signature(x = "dgCMatrix"),

-          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...)

-            dgCMatrix_colMeans2(t(x), na_rm = na.rm))

+          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

+  if(! is.null(rows)){

+    x <- x[rows, , drop = FALSE]

+  }

+  if(! is.null(cols)){

+    x <- x[, cols, drop = FALSE]

+  }

+  dgCMatrix_colMeans2(t(x), na_rm = na.rm)

+})

 # Median

-#' @rdname colMedians

+#' @rdname colMedians-dgCMatrix-method

 #' @export

-setGeneric("rowMedians", function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-  matrixStats::rowMedians(as.matrix(x), rows = rows, cols = cols, na.rm = na.rm, ...)

+setMethod("rowMedians", signature(x = "dgCMatrix"),

+          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

+  if(! is.null(rows)){

+    x <- x[rows, , drop = FALSE]

+  }

+  if(! is.null(cols)){

+    x <- x[, cols, drop = FALSE]

+  }

+  dgCMatrix_colMedians(t(x), na_rm = na.rm)

 })

-#' @rdname colMedians

-#' @export

-setMethod("rowMedians", signature(x = "dgCMatrix"),

-          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...)

-            dgCMatrix_colMedians(t(x), na_rm = na.rm))

 # Vars

-#' @rdname colVars

-#' @export

-setGeneric("rowVars", function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-  matrixStats::rowVars(as.matrix(x), rows = rows, cols = cols, na.rm = na.rm, ...)

-})

-

-#' @rdname colVars

+#' @rdname colVars-dgCMatrix-method

 #' @export

 setMethod("rowVars", signature(x = "dgCMatrix"),

-          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...)

-            dgCMatrix_colVars(t(x), na_rm = na.rm))

+          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

+  if(! is.null(rows)){

+    x <- x[rows, , drop = FALSE]

+  }

+  if(! is.null(cols)){

+    x <- x[, cols, drop = FALSE]

+  }

+  dgCMatrix_colVars(t(x), na_rm = na.rm)

+})

 # Sds

-#' @rdname colSds

-#' @export

-setGeneric("rowSds", function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-  matrixStats::rowSds(as.matrix(x), rows = rows, cols = cols, na.rm = na.rm, ...)

-})

-

-#' @rdname colSds

+#' @rdname colSds-dgCMatrix-method

 #' @export

 setMethod("rowSds", signature(x = "dgCMatrix"),

-          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...)

-            sqrt(dgCMatrix_colVars(t(x), na_rm = na.rm)))

+          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

+  if(! is.null(rows)){

+    x <- x[rows, , drop = FALSE]

+  }

+  if(! is.null(cols)){

+    x <- x[, cols, drop = FALSE]

+  }

+  sqrt(dgCMatrix_colVars(t(x), na_rm = na.rm))

+})

@@ -124,32 +130,34 @@ setMethod("rowProds", signature(x = "dgCMatrix"),

 # Min

-#' @rdname colMins

-#' @export

-setGeneric("rowMins", function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-  matrixStats::rowMins(as.matrix(x), rows = rows, cols = cols, na.rm = na.rm, ...)

-})

-

-#' @rdname colMins

+#' @rdname colMins-dgCMatrix-method

 #' @export

 setMethod("rowMins", signature(x = "dgCMatrix"),

-          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...)

-            dgCMatrix_colMins(t(x), na_rm = na.rm))

+          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

+  if(! is.null(rows)){

+    x <- x[rows, , drop = FALSE]

+  }

+  if(! is.null(cols)){

+    x <- x[, cols, drop = FALSE]

+  }

+  dgCMatrix_colMins(t(x), na_rm = na.rm)

+})

 # Max

-#' @rdname colMaxs

-#' @export

-setGeneric("rowMaxs", function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-  matrixStats::rowMaxs(as.matrix(x), rows = rows, cols = cols, na.rm = na.rm, ...)

-})

-

-#' @rdname colMaxs

+#' @rdname colMaxs-dgCMatrix-method

 #' @export

 setMethod("rowMaxs", signature(x = "dgCMatrix"),

-          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...)

-            dgCMatrix_colMaxs(t(x), na_rm = na.rm))

+          function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

+  if(! is.null(rows)){

+    x <- x[rows, , drop = FALSE]

+  }

+  if(! is.null(cols)){

+    x <- x[, cols, drop = FALSE]

+  }

+  dgCMatrix_colMaxs(t(x), na_rm = na.rm)

+})

 # OrderStats

@@ -396,21 +404,21 @@ setMethod("rowIQRs", signature(x = "dgCMatrix"),

 # Ranges

-#' @rdname colRanges

-#' @export

-setGeneric("rowRanges", function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-  matrixStats::rowRanges(as.matrix(x), rows = rows, cols = cols, na.rm = na.rm, ...)

-})

-

-#' @rdname colRanges

+#' @rdname colRanges-dgCMatrix-method

 #' @export

 setMethod("rowRanges", signature(x = "dgCMatrix"),

           function(x, rows = NULL, cols = NULL, na.rm=FALSE, ...){

-            tx <- t(x)

-            row_max <- colMaxs(tx, rows, cols, na.rm = na.rm)

-            row_max <- colMins(tx, rows, cols, na.rm = na.rm)

-            unname(cbind(row_max, row_max))

-          })

+  if(! is.null(rows)){

+    x <- x[rows, , drop = FALSE]

+  }

+  if(! is.null(cols)){

+    x <- x[, cols, drop = FALSE]

+  }

+  tx <- t(x)

+  row_max <- colMaxs(tx, rows, cols, na.rm = na.rm)

+  row_max <- colMins(tx, rows, cols, na.rm = na.rm)

+  unname(cbind(row_max, row_max))

+})

new file mode 100644

@@ -0,0 +1,59 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/methods.R, R/methods_row.R

+\docType{methods}

+\name{colMaxs,dgCMatrix-method}

+\alias{colMaxs,dgCMatrix-method}

+\alias{rowMaxs,dgCMatrix-method}

+\title{Calculates the maximum for each row (column) of a matrix-like object}

+\usage{

+\S4method{colMaxs}{dgCMatrix}(x, rows = NULL, cols = NULL,

+  na.rm = FALSE, ...)

+

+\S4method{rowMaxs}{dgCMatrix}(x, rows = NULL, cols = NULL,

+  na.rm = FALSE, ...)

+}

+\arguments{

+\item{x}{An NxK matrix-like object.}

+

+\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or

+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}

+

+\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or

+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}

+

+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s

+are excluded first, otherwise not.}

+

+\item{...}{Additional arguments passed to specific methods.}

+}

+\value{

+Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of

+length N (K).

+}

+\description{

+Calculates the maximum for each row (column) of a matrix-like object.

+}

+\details{

+The S4 methods for \code{x} of type \code{\link[base]{matrix}} or

+\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowMaxs}}

+/ \code{matrixStats::\link[matrixStats]{colMaxs}}.

+}

+\examples{

+mat <- matrix(rnorm(15), nrow = 5, ncol = 3)

+  mat[2, 1] <- NA

+  mat[3, 3] <- Inf

+  mat[4, 1] <- 0

+  

+  print(mat)

+  

+  rowMaxs(mat)

+  colMaxs(mat)

+}

+\seealso{

+\itemize{

+\item \code{matrixStats::\link[matrixStats]{rowMaxs}()} and

+  \code{matrixStats::\link[matrixStats]{colMaxs}()} which are used when

+  the input is a \code{matrix} or \code{numeric} vector.

+\item For min estimates, see \code{\link{rowMins}()}.

+}

+}

deleted file mode 100644

@@ -1,50 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/methods.R, R/methods_row.R

-\docType{methods}

-\name{colMaxs}

-\alias{colMaxs}

-\alias{colMaxs,dgCMatrix-method}

-\alias{rowMaxs}

-\alias{rowMaxs,dgCMatrix-method}

-\title{Gets the range of values in each row (column) of a matrix}

-\usage{

-colMaxs(x, rows = NULL, cols = NULL, na.rm = FALSE, ...)

-

-\S4method{colMaxs}{dgCMatrix}(x, rows = NULL, cols = NULL,

-  na.rm = FALSE, ...)

-

-rowMaxs(x, rows = NULL, cols = NULL, na.rm = FALSE, ...)

-

-\S4method{rowMaxs}{dgCMatrix}(x, rows = NULL, cols = NULL,

-  na.rm = FALSE, ...)

-}

-\arguments{

-\item{x}{A \code{\link[base]{numeric}} NxK \code{\link[base]{matrix}}.}

-

-\item{rows}{A \code{\link[base]{vector}} indicating subset of rows

-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no subsetting

-is done.}

-

-\item{cols}{A \code{\link[base]{vector}} indicating subset of rows

-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no subsetting

-is done.}

-

-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s

-are excluded first, otherwise not.}

-

-\item{...}{Not used.}

-}

-\value{

-\code{rowRanges()} (\code{colRanges()}) returns a

-\code{\link[base]{numeric}} Nx2 (Kx2) \code{\link[base]{matrix}}, where N

-(K) is the number of rows (columns) for which the ranges are calculated.

-

-\code{rowMins()/rowMaxs()} (\code{colMins()/colMaxs()}) returns a

-\code{\link[base]{numeric}} \code{\link[base]{vector}} of length N (K).

-}

-\description{

-Gets the range of values in each row (column) of a matrix.

-}

-\seealso{

-\code{\link{rowOrderStats}}() and \code{\link[base]{pmin.int}}().

-}

new file mode 100644

@@ -0,0 +1,61 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/methods.R, R/methods_row.R

+\docType{methods}

+\name{colMeans2,dgCMatrix-method}

+\alias{colMeans2,dgCMatrix-method}

+\alias{rowMeans2,dgCMatrix-method}

+\title{Calculates the mean for each row (column) of a matrix-like object}

+\usage{

+\S4method{colMeans2}{dgCMatrix}(x, rows = NULL, cols = NULL,

+  na.rm = FALSE, ...)

+

+\S4method{rowMeans2}{dgCMatrix}(x, rows = NULL, cols = NULL,

+  na.rm = FALSE, ...)

+}

+\arguments{

+\item{x}{An NxK matrix-like object.}

+

+\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or

+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}

+

+\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or

+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}

+

+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s

+are excluded first, otherwise not.}

+

+\item{...}{Additional arguments passed to specific methods.}

+}

+\value{

+Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of

+length N (K).

+}

+\description{

+Calculates the mean for each row (column) of a matrix-like object.

+}

+\details{

+The S4 methods for \code{x} of type \code{\link[base]{matrix}} or

+\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowMeans2}}

+/ \code{matrixStats::\link[matrixStats]{colMeans2}}.

+}

+\examples{

+mat <- matrix(rnorm(15), nrow = 5, ncol = 3)

+  mat[2, 1] <- NA

+  mat[3, 3] <- Inf

+  mat[4, 1] <- 0

+  

+  print(mat)

+  

+  rowMeans2(mat)

+  colMeans2(mat)

+}

+\seealso{

+\itemize{

+\item \code{matrixStats::\link[matrixStats]{rowMeans2}()} and

+  \code{matrixStats::\link[matrixStats]{colMeans2}()} which are used when

+  the input is a \code{matrix} or \code{numeric} vector.

+\item See also \code{\link[base:colSums]{rowMeans}()} for the

+  corresponding function in base R.

+\item For variance estimates, see \code{\link{rowVars}()}.

+}

+}

deleted file mode 100644

@@ -1,48 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/methods.R, R/methods_row.R

-\docType{methods}

-\name{colMeans2}

-\alias{colMeans2}

-\alias{colMeans2,dgCMatrix-method}

-\alias{rowMeans2}

-\alias{rowMeans2,dgCMatrix-method}

-\title{Calculates the mean for each row (column) in a matrix}

-\usage{

-colMeans2(x, rows = NULL, cols = NULL, na.rm = FALSE, ...)

-

-\S4method{colMeans2}{dgCMatrix}(x, rows = NULL, cols = NULL,

-  na.rm = FALSE, ...)

-

-rowMeans2(x, rows = NULL, cols = NULL, na.rm = FALSE, ...)

-

-\S4method{rowMeans2}{dgCMatrix}(x, rows = NULL, cols = NULL,

-  na.rm = FALSE, ...)

-}

-\arguments{

-\item{x}{A \code{\link[base]{numeric}} or a \code{\link[base]{logical}}

-NxK \code{\link[base]{matrix}}.}

-

-\item{rows}{A \code{\link[base]{vector}} indicating subset of rows

-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no subsetting

-is done.}

-

-\item{cols}{A \code{\link[base]{vector}} indicating subset of rows

-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no subsetting

-is done.}

-

-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s

-are excluded first, otherwise not.}

-

-\item{...}{Not used.}

-}

-\value{

-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of

-length N (K).

-}

-\description{

-Calculates the mean for each row (column) in a matrix.

-}

-\details{

-The implementation of \code{rowMeans2()} and \code{colMeans2()} is

-optimized for both speed and memory.

-}

new file mode 100644

@@ -0,0 +1,60 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/methods.R, R/methods_row.R

+\docType{methods}

+\name{colMedians,dgCMatrix-method}

+\alias{colMedians,dgCMatrix-method}

+\alias{rowMedians,dgCMatrix-method}

+\title{Calculates the median for each row (column) of a matrix-like object}

+\usage{

+\S4method{colMedians}{dgCMatrix}(x, rows = NULL, cols = NULL,

+  na.rm = FALSE, ...)

+

+\S4method{rowMedians}{dgCMatrix}(x, rows = NULL, cols = NULL,

+  na.rm = FALSE, ...)

+}

+\arguments{

+\item{x}{An NxK matrix-like object.}

+

+\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or

+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}

+

+\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or

+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}

+

+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s

+are excluded first, otherwise not.}

+

+\item{...}{Additional arguments passed to specific methods.}

+}

+\value{

+Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of

+length N (K).

+}

+\description{

+Calculates the median for each row (column) of a matrix-like object.

+}

+\details{

+The S4 methods for \code{x} of type \code{\link[base]{matrix}} or

+\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowMedians}}

+/ \code{matrixStats::\link[matrixStats]{colMedians}}.

+}

+\examples{

+mat <- matrix(rnorm(15), nrow = 5, ncol = 3)

+  mat[2, 1] <- NA

+  mat[3, 3] <- Inf

+  mat[4, 1] <- 0

+  

+  print(mat)

+  

+  rowMedians(mat)

+  colMedians(mat)

+}

+\seealso{

+\itemize{

+\item \code{matrixStats::\link[matrixStats]{rowMedians}()} and

+  \code{matrixStats::\link[matrixStats]{colMedians}()} which are used when

+  the input is a \code{matrix} or \code{numeric} vector.

+\item For mean estimates, see \code{\link{rowMeans2}()} and

+  \code{\link[base:colSums]{rowMeans}()}.

+}

+}

deleted file mode 100644

@@ -1,59 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/methods.R, R/methods_row.R

-\docType{methods}

-\name{colMedians}

-\alias{colMedians}

-\alias{colMedians,dgCMatrix-method}

-\alias{rowMedians}

-\alias{rowMedians,dgCMatrix-method}

-\title{Calculates the median for each row (column) in a matrix}

-\usage{

-colMedians(x, rows = NULL, cols = NULL, na.rm = FALSE, ...)

-

-\S4method{colMedians}{dgCMatrix}(x, rows = NULL, cols = NULL,

-  na.rm = FALSE, ...)

-

-rowMedians(x, rows = NULL, cols = NULL, na.rm = FALSE, ...)

-

-\S4method{rowMedians}{dgCMatrix}(x, rows = NULL, cols = NULL,

-  na.rm = FALSE, ...)

-}

-\arguments{

-\item{x}{A \code{\link[base]{numeric}} NxK \code{\link[base]{matrix}}.}

-

-\item{rows}{A \code{\link[base]{vector}} indicating subset of rows

-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no subsetting

-is done.}

-

-\item{cols}{A \code{\link[base]{vector}} indicating subset of rows

-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no subsetting

-is done.}

-

-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s

-are excluded first, otherwise not.}

-

-\item{...}{Not used.}

-}

-\value{

-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of

-length N (K).

-}

-\description{

-Calculates the median for each row (column) in a matrix.

-}

-\details{

-The implementation of \code{rowMedians()} and \code{colMedians()} is

-optimized for both speed and memory.  To avoid coercing to

-\code{\link[base]{double}}s (and hence memory allocation), there is a

-special implementation for \code{\link[base]{integer}} matrices.  That is,

-if \code{x} is an \code{\link[base]{integer}} \code{\link[base]{matrix}},

-then \code{rowMedians(as.double(x))} (\code{rowMedians(as.double(x))}) would

-require three times the memory of \code{rowMedians(x)}

-(\code{colMedians(x)}), but all this is avoided.

-}

-\seealso{

-See \code{\link{rowWeightedMedians}()} and

-\code{colWeightedMedians()} for weighted medians.

-For mean estimates, see \code{\link{rowMeans2}()} and

-\code{\link[base:colSums]{rowMeans}()}.

-}

new file mode 100644

@@ -0,0 +1,59 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/methods.R, R/methods_row.R

+\docType{methods}

+\name{colMins,dgCMatrix-method}

+\alias{colMins,dgCMatrix-method}

+\alias{rowMins,dgCMatrix-method}

+\title{Calculates the minimum for each row (column) of a matrix-like object}

+\usage{

+\S4method{colMins}{dgCMatrix}(x, rows = NULL, cols = NULL,

+  na.rm = FALSE, ...)

+

+\S4method{rowMins}{dgCMatrix}(x, rows = NULL, cols = NULL,

+  na.rm = FALSE, ...)

+}

+\arguments{

+\item{x}{An NxK matrix-like object.}

+

+\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or

+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}

+

+\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or

+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}

+

+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s

+are excluded first, otherwise not.}

+

+\item{...}{Additional arguments passed to specific methods.}

+}

+\value{

+Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of

+length N (K).

+}

+\description{

+Calculates the minimum for each row (column) of a matrix-like object.

+}

+\details{

+The S4 methods for \code{x} of type \code{\link[base]{matrix}} or

+\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowMins}}

+/ \code{matrixStats::\link[matrixStats]{colMins}}.

+}

+\examples{

+mat <- matrix(rnorm(15), nrow = 5, ncol = 3)

+  mat[2, 1] <- NA

+  mat[3, 3] <- Inf

+  mat[4, 1] <- 0

+  

+  print(mat)

+  

+  rowMins(mat)

+  colMins(mat)

+}

+\seealso{

+\itemize{

+\item \code{matrixStats::\link[matrixStats]{rowMins}()} and

+  \code{matrixStats::\link[matrixStats]{colMins}()} which are used when

+  the input is a \code{matrix} or \code{numeric} vector.

+\item For max estimates, see \code{\link{rowMaxs}()}.

+}

+}