1. sparseMatrixStats
  2. man
  3. colCollapse-dgCMatrix-method.Rd
Browse code

Enable a lot of functions to handle logical input

* colVars
* colSds
* colLogSumExps
* colProds
* colWeightedMeans
* colWeigthedVars
* colWeightedSds
* colCounts
* colAnyNAs
* colAnys
* colAlls
* colCollapse
* colQuantiles
* colTabulates
* colIQRs
* colCumsums
* colCumprods
* colAvgsPerRowSet

const-ae authored on 18/05/2020 13:35:58
Showing 1 changed files
man/colCollapse-dgCMatrix-method.Rd
History View file @ d975812
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deleted file mode 100644
... ... 
@@ -1,57 +0,0 @@
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-% Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/methods.R, R/methods_row.R
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-\name{colCollapse,dgCMatrix-method}
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-\alias{colCollapse,dgCMatrix-method}
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-\alias{rowCollapse,dgCMatrix-method}
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-\title{Extract one cell from each row (column) of a matrix-like object}
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-\usage{
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-\S4method{colCollapse}{dgCMatrix}(x, idxs, cols = NULL)
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-
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-\S4method{rowCollapse}{dgCMatrix}(x, idxs, rows = NULL)
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-}
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-\arguments{
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-\item{x}{An NxK matrix-like object.}
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-
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-\item{idxs}{An index \code{\link{vector}} with the position to extract.
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-It is recycled to match the number of rows (column)}
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-
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-\item{cols}{A \code{\link{vector}} indicating the subset of rows
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-(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
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-done.}
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-
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-\item{rows}{A \code{\link{vector}} indicating the subset of rows
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-(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
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-done.}
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-}
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-\value{
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-Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
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-}
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-\description{
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-Extract one cell from each row (column) of a matrix-like object.
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-}
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-\details{
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-The S4 methods for \code{x} of type \code{\link{matrix}},
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-\code{\link{array}}, or \code{\link{numeric}} call
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-\code{matrixStats::\link[matrixStats]{rowCollapse}}
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-/ \code{matrixStats::\link[matrixStats:rowCollapse]{colCollapse}}.
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-}
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-\examples{
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-mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
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-  mat[2, 1] <- NA
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-  mat[3, 3] <- Inf
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-  mat[4, 1] <- 0
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-
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-  print(mat)
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-
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-  rowCollapse(mat, idxs = 2)
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-  rowCollapse(mat, idxs = c(1,1,2,3,2))
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-
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-  colCollapse (mat, idxs = 4)
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-}
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-\seealso{
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-\itemize{
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-\item \code{matrixStats::\link[matrixStats]{rowCollapse}()} and
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-\code{matrixStats::\link[matrixStats:rowCollapse]{colCollapse}()}
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-which are used when the input is a \code{matrix} or \code{numeric} vector.
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-}
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-}
Browse code

Bring documentation in line with updates from MatrixGenerics

See https://github.com/Bioconductor/MatrixGenerics/issues/11
for more information

const-ae authored on 24/04/2020 07:36:21
Showing 1 changed files
man/colCollapse-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -12,29 +12,28 @@
12 12 
 \arguments{
13 13 
 \item{x}{An NxK matrix-like object.}
14 14
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-\item{idxs}{An index \code{\link[base]{vector}} with the position to extract.
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+\item{idxs}{An index \code{\link{vector}} with the position to extract.
16 16 
 It is recycled to match the number of rows (column)}
17 17
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-\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
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-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
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-subsetting is done.}
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+\item{cols}{A \code{\link{vector}} indicating the subset of rows
19 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
20 
+done.}
21 21
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-\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
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-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
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-subsetting is done.}
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+\item{rows}{A \code{\link{vector}} indicating the subset of rows
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+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
24 
+done.}
25 25 
 }
26 26 
 \value{
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-Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
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-length N (K).
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+Returns a \code{\link{numeric}} \code{\link{vector}} of length N (K).
29 28 
 }
30 29 
 \description{
31 30 
 Extract one cell from each row (column) of a matrix-like object.
32 31 
 }
33 32 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
35 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
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+The S4 methods for \code{x} of type \code{\link{matrix}},
34 
+\code{\link{array}}, or \code{\link{numeric}} call
36 35 
 \code{matrixStats::\link[matrixStats]{rowCollapse}}
37 
-/ \code{matrixStats::\link[matrixStats]{colCollapse}}.
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+/ \code{matrixStats::\link[matrixStats:rowCollapse]{colCollapse}}.
38 37 
 }
39 38 
 \examples{
40 39 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -52,7 +51,7 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
52 51 
 \seealso{
53 52 
 \itemize{
54 53 
 \item \code{matrixStats::\link[matrixStats]{rowCollapse}()} and
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-\code{matrixStats::\link[matrixStats]{colCollapse}()} which are used when
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-the input is a \code{matrix} or \code{numeric} vector.
54 
+\code{matrixStats::\link[matrixStats:rowCollapse]{colCollapse}()}
55 
+which are used when the input is a \code{matrix} or \code{numeric} vector.
57 56 
 }
58 57 
 }
Browse code

Remove superfluous ... from method signatures

const-ae authored on 03/04/2020 10:39:05
Showing 1 changed files
man/colCollapse-dgCMatrix-method.Rd
History View file @ 8ee76bd
... ... 
@@ -5,9 +5,9 @@
5 5 
 \alias{rowCollapse,dgCMatrix-method}
6 6 
 \title{Extract one cell from each row (column) of a matrix-like object}
7 7 
 \usage{
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-\S4method{colCollapse}{dgCMatrix}(x, idxs = idxs, cols = NULL, ...)
8 
+\S4method{colCollapse}{dgCMatrix}(x, idxs, cols = NULL)
9 9
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-\S4method{rowCollapse}{dgCMatrix}(x, idxs, rows = NULL, ...)
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+\S4method{rowCollapse}{dgCMatrix}(x, idxs, rows = NULL)
11 11 
 }
12 12 
 \arguments{
13 13 
 \item{x}{An NxK matrix-like object.}
... ... 
@@ -19,8 +19,6 @@ It is recycled to match the number of rows (column)}
19 19 
 (and/or columns) to operate over. If \code{\link[base]{NULL}}, no
20 20 
 subsetting is done.}
21 21
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-\item{...}{Additional arguments passed to specific methods.}
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-
24 22 
 \item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
25 23 
 (and/or columns) to operate over. If \code{\link[base]{NULL}}, no
26 24 
 subsetting is done.}
Browse code

Bring documentation in line with MatrixGenerics

const-ae authored on 03/04/2020 10:19:46
Showing 1 changed files
man/colCollapse-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -15,24 +15,27 @@
15 15 
 \item{idxs}{An index \code{\link[base]{vector}} with the position to extract.
16 16 
 It is recycled to match the number of rows (column)}
17 17
18 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
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+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
19 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
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+subsetting is done.}
20 21
21 22 
 \item{...}{Additional arguments passed to specific methods.}
22 23
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-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
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-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
24 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
25 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
26 
+subsetting is done.}
25 27 
 }
26 28 
 \value{
27 29 
 Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
28 30 
 length N (K).
29 31 
 }
30 32 
 \description{
31 
-Extract one cell from each row (column) of a matrix-like object
33 
+Extract one cell from each row (column) of a matrix-like object.
32 34 
 }
33 35 
 \details{
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-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
35 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowCollapse}}
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+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
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+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
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+\code{matrixStats::\link[matrixStats]{rowCollapse}}
36 39 
 / \code{matrixStats::\link[matrixStats]{colCollapse}}.
37 40 
 }
38 41 
 \examples{
Browse code

Use MatrixGenerics for all rowXXX functions

const-ae authored on 16/03/2020 20:22:08
Showing 1 changed files
man/colCollapse-dgCMatrix-method.Rd
History View file @ 17c056e
... ... 
@@ -1,10 +1,13 @@
1 1 
 % Generated by roxygen2: do not edit by hand
2 
-% Please edit documentation in R/methods.R
2 
+% Please edit documentation in R/methods.R, R/methods_row.R
3 3 
 \name{colCollapse,dgCMatrix-method}
4 4 
 \alias{colCollapse,dgCMatrix-method}
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+\alias{rowCollapse,dgCMatrix-method}
5 6 
 \title{Extract one cell from each row (column) of a matrix-like object}
6 7 
 \usage{
7 8 
 \S4method{colCollapse}{dgCMatrix}(x, idxs = idxs, cols = NULL, ...)
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+
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+\S4method{rowCollapse}{dgCMatrix}(x, idxs, rows = NULL, ...)
8 11 
 }
9 12 
 \arguments{
10 13 
 \item{x}{An NxK matrix-like object.}
... ... 
@@ -16,6 +19,9 @@ It is recycled to match the number of rows (column)}
16 19 
 columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
17 20
18 21 
 \item{...}{Additional arguments passed to specific methods.}
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+
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+\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
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+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
19 25 
 }
20 26 
 \value{
21 27 
 Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
Browse code

Use MatrixGenerics for all colXXX functions

const-ae authored on 16/03/2020 20:00:12
Showing 1 changed files
man/colCollapse-dgCMatrix-method.Rd
History View file @ ef7cdb2
1 1 
new file mode 100644
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@@ -0,0 +1,51 @@
1 
+% Generated by roxygen2: do not edit by hand
2 
+% Please edit documentation in R/methods.R
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+\name{colCollapse,dgCMatrix-method}
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+\alias{colCollapse,dgCMatrix-method}
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+\title{Extract one cell from each row (column) of a matrix-like object}
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+\usage{
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+\S4method{colCollapse}{dgCMatrix}(x, idxs = idxs, cols = NULL, ...)
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+}
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+\arguments{
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+\item{x}{An NxK matrix-like object.}
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+
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+\item{idxs}{An index \code{\link[base]{vector}} with the position to extract.
13 
+It is recycled to match the number of rows (column)}
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+
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+\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
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+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
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+
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+\item{...}{Additional arguments passed to specific methods.}
19 
+}
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+\value{
21 
+Returns a \code{\link[base]{numeric}} \code{\link[base]{vector}} of
22 
+length N (K).
23 
+}
24 
+\description{
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+Extract one cell from each row (column) of a matrix-like object
26 
+}
27 
+\details{
28 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
29 
+\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowCollapse}}
30 
+/ \code{matrixStats::\link[matrixStats]{colCollapse}}.
31 
+}
32 
+\examples{
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+mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
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+  mat[2, 1] <- NA
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+  mat[3, 3] <- Inf
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+  mat[4, 1] <- 0
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+
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+  print(mat)
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+
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+  rowCollapse(mat, idxs = 2)
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+  rowCollapse(mat, idxs = c(1,1,2,3,2))
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+
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+  colCollapse (mat, idxs = 4)
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+}
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+\seealso{
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+\itemize{
47 
+\item \code{matrixStats::\link[matrixStats]{rowCollapse}()} and
48 
+\code{matrixStats::\link[matrixStats]{colCollapse}()} which are used when
49 
+the input is a \code{matrix} or \code{numeric} vector.
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+}
51 
+}