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

Add useNames argument

This makes sparseMatrixStats compatible with v0.60 of matrixStats

In this commit
* I introduce a set of function called `set_result_names()`
that take the internally computed result and add correct names if needed
* Add colnames to the matrices of the unit tests
* Update the documentation to reflect the changed method signatures

const-ae authored on 05/08/2021 13:05:38
Showing 1 changed files
man/colRanges-dgCMatrix-method.Rd
History View file @ eaab674
... ... 
@@ -6,9 +6,9 @@
6 6 
 \title{Calculates the minimum and maximum for each row (column) of a matrix-like
7 7 
 object}
8 8 
 \usage{
9 
-\S4method{colRanges}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE)
9 
+\S4method{colRanges}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE, useNames = NA)
10 10
11 
-\S4method{rowRanges}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE)
11 
+\S4method{rowRanges}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE, useNames = NA)
12 12 
 }
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
... ... 
@@ -23,6 +23,8 @@ done.}
23 23
24 24 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
25 25 
 are excluded first, otherwise not.}
26 
+
27 
+\item{useNames}{If \code{\link{NA}}, the default behavior of the function about naming support is remained. If \code{\link{FALSE}}, no naming support is done. Else if \code{\link{TRUE}}, names attributes of result are set.}
26 28 
 }
27 29 
 \value{
28 30 
 a \code{\link{numeric}} \code{Nx2} (\code{Kx2})
Browse code

Update documentation to latest version of MatrixGenerics

const-ae authored on 21/05/2020 11:07:40
Showing 1 changed files
man/colRanges-dgCMatrix-method.Rd
History View file @ fd0ef25
... ... 
@@ -36,8 +36,8 @@ object.
36 36 
 \details{
37 37 
 The S4 methods for \code{x} of type \code{\link{matrix}},
38 38 
 \code{\link{array}}, or \code{\link{numeric}} call
39 
-\code{matrixStats::\link[matrixStats]{rowRanges}}
40 
-/ \code{matrixStats::\link[matrixStats:rowRanges]{colRanges}}.
39 
+\code{matrixStats::rowRanges}
40 
+/ \code{matrixStats::colRanges}.
41 41 
 }
42 42 
 \examples{
43 43 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
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/colRanges-dgCMatrix-method.Rd
History View file @ 7f055a6
... ... 
@@ -13,19 +13,19 @@ object}
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
15 15
16 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
17 
-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
18 
-subsetting is done.}
16 
+\item{rows}{A \code{\link{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
18 
+done.}
19 19
20 
-\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
21 
-(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
22 
-subsetting is done.}
20 
+\item{cols}{A \code{\link{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link{NULL}}, no subsetting is
22 
+done.}
23 23
24 
-\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
24 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link{NA}}s
25 25 
 are excluded first, otherwise not.}
26 26 
 }
27 27 
 \value{
28 
-a \code{\link[base]{numeric}} \code{Nx2} (\code{Kx2})
28 
+a \code{\link{numeric}} \code{Nx2} (\code{Kx2})
29 29 
 \code{\link{matrix}}, where N (K) is the number of rows (columns) for
30 30 
 which the ranges are calculated.
31 31 
 }
... ... 
@@ -34,10 +34,10 @@ Calculates the minimum and maximum for each row (column) of a matrix-like
34 34 
 object.
35 35 
 }
36 36 
 \details{
37 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}},
38 
-\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
37 
+The S4 methods for \code{x} of type \code{\link{matrix}},
38 
+\code{\link{array}}, or \code{\link{numeric}} call
39 39 
 \code{matrixStats::\link[matrixStats]{rowRanges}}
40 
-/ \code{matrixStats::\link[matrixStats]{colRanges}}.
40 
+/ \code{matrixStats::\link[matrixStats:rowRanges]{colRanges}}.
41 41 
 }
42 42 
 \examples{
43 43 
 mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
... ... 
@@ -53,10 +53,10 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
53 53 
 \seealso{
54 54 
 \itemize{
55 55 
 \item \code{matrixStats::\link[matrixStats]{rowRanges}()} and
56 
-\code{matrixStats::\link[matrixStats]{colRanges}()} which are used when
57 
-the input is a \code{matrix} or \code{numeric} vector.
56 
+\code{matrixStats::\link[matrixStats:rowRanges]{colRanges}()} which are
57 
+used when the input is a \code{matrix} or \code{numeric} vector.
58 58 
 \item For max estimates, see \code{\link[MatrixGenerics]{rowMaxs}()}.
59 59 
 \item For min estimates, see \code{\link[MatrixGenerics]{rowMins}()}.
60 
-\item \code{base::\link[base]{range}()}.
60 
+\item \code{base::\link{range}()}.
61 61 
 }
62 62 
 }
Browse code

Remove superfluous ... from method signatures

const-ae authored on 03/04/2020 10:39:05
Showing 1 changed files
man/colRanges-dgCMatrix-method.Rd
History View file @ 8ee76bd
... ... 
@@ -6,9 +6,9 @@
6 6 
 \title{Calculates the minimum and maximum for each row (column) of a matrix-like
7 7 
 object}
8 8 
 \usage{
9 
-\S4method{colRanges}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE, ...)
9 
+\S4method{colRanges}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE)
10 10
11 
-\S4method{rowRanges}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE, ...)
11 
+\S4method{rowRanges}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE)
12 12 
 }
13 13 
 \arguments{
14 14 
 \item{x}{An NxK matrix-like object.}
... ... 
@@ -23,8 +23,6 @@ subsetting is done.}
23 23
24 24 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
25 25 
 are excluded first, otherwise not.}
26 
-
27 
-\item{...}{Additional arguments passed to specific methods.}
28 26 
 }
29 27 
 \value{
30 28 
 a \code{\link[base]{numeric}} \code{Nx2} (\code{Kx2})
Browse code

Bring documentation in line with MatrixGenerics

const-ae authored on 03/04/2020 10:19:46
Showing 1 changed files
man/colRanges-dgCMatrix-method.Rd
History View file @ 2a92411
... ... 
@@ -3,7 +3,8 @@
3 3 
 \name{colRanges,dgCMatrix-method}
4 4 
 \alias{colRanges,dgCMatrix-method}
5 5 
 \alias{rowRanges,dgCMatrix-method}
6 
-\title{Calculates the minimum and maximum for each row (column) of a matrix-like object}
6 
+\title{Calculates the minimum and maximum for each row (column) of a matrix-like
7 
+object}
7 8 
 \usage{
8 9 
 \S4method{colRanges}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE, ...)
9 10
... ... 
@@ -12,11 +13,13 @@
12 13 
 \arguments{
13 14 
 \item{x}{An NxK matrix-like object.}
14 15
15 
-\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
16 
-columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
16 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset of rows
17 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
18 
+subsetting is done.}
17 19
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.}
20 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset of rows
21 
+(and/or columns) to operate over. If \code{\link[base]{NULL}}, no
22 
+subsetting is done.}
20 23
21 24 
 \item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
22 25 
 are excluded first, otherwise not.}
... ... 
@@ -24,15 +27,18 @@ are excluded first, otherwise not.}
24 27 
 \item{...}{Additional arguments passed to specific methods.}
25 28 
 }
26 29 
 \value{
27 
-a \code{\link[base]{numeric}} \code{Nx2} (\code{Kx2}) \code{\link{matrix}}, where
28 
-N (K) is the number of rows (columns) for which the ranges are calculated.
30 
+a \code{\link[base]{numeric}} \code{Nx2} (\code{Kx2})
31 
+\code{\link{matrix}}, where N (K) is the number of rows (columns) for
32 
+which the ranges are calculated.
29 33 
 }
30 34 
 \description{
31 
-Calculates the minimum and maximum for each row (column) of a matrix-like object.
35 
+Calculates the minimum and maximum for each row (column) of a matrix-like
36 
+object.
32 37 
 }
33 38 
 \details{
34 
-The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
35 
-\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowRanges}}
39 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}},
40 
+\code{\link[base]{array}}, or \code{\link[base]{numeric}} call
41 
+\code{matrixStats::\link[matrixStats]{rowRanges}}
36 42 
 / \code{matrixStats::\link[matrixStats]{colRanges}}.
37 43 
 }
38 44 
 \examples{
... ... 
@@ -53,6 +59,6 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
53 59 
 the input is a \code{matrix} or \code{numeric} vector.
54 60 
 \item For max estimates, see \code{\link[MatrixGenerics]{rowMaxs}()}.
55 61 
 \item For min estimates, see \code{\link[MatrixGenerics]{rowMins}()}.
56 
-\item \link{range}
62 
+\item \code{base::\link[base]{range}()}.
57 63 
 }
58 64 
 }
Browse code

Use MatrixGenerics for all colXXX functions

const-ae authored on 16/03/2020 20:00:12
Showing 1 changed files
man/colRanges-dgCMatrix-method.Rd
History View file @ ef7cdb2
... ... 
@@ -1,16 +1,13 @@
1 1 
 % Generated by roxygen2: do not edit by hand
2 2 
 % Please edit documentation in R/methods.R, R/methods_row.R
3 
-\docType{methods}
4 3 
 \name{colRanges,dgCMatrix-method}
5 4 
 \alias{colRanges,dgCMatrix-method}
6 5 
 \alias{rowRanges,dgCMatrix-method}
7 
-\title{Calculates the mininum and maximum for each row (column) of a matrix-like object}
6 
+\title{Calculates the minimum and maximum for each row (column) of a matrix-like object}
8 7 
 \usage{
9 
-\S4method{colRanges}{dgCMatrix}(x, rows = NULL, cols = NULL,
10 
-  na.rm = FALSE, ...)
8 
+\S4method{colRanges}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE, ...)
11 9
12 
-\S4method{rowRanges}{dgCMatrix}(x, rows = NULL, cols = NULL,
13 
-  na.rm = FALSE, ...)
10 
+\S4method{rowRanges}{dgCMatrix}(x, rows = NULL, cols = NULL, na.rm = FALSE, ...)
14 11 
 }
15 12 
 \arguments{
16 13 
 \item{x}{An NxK matrix-like object.}
... ... 
@@ -28,10 +25,10 @@ are excluded first, otherwise not.}
28 25 
 }
29 26 
 \value{
30 27 
 a \code{\link[base]{numeric}} \code{Nx2} (\code{Kx2}) \code{\link{matrix}}, where
31 
-  N (K) is the number of rows (columns) for which the ranges are calculated.
28 
+N (K) is the number of rows (columns) for which the ranges are calculated.
32 29 
 }
33 30 
 \description{
34 
-Calculates the mininum and maximum for each row (column) of a matrix-like object.
31 
+Calculates the minimum and maximum for each row (column) of a matrix-like object.
35 32 
 }
36 33 
 \details{
37 34 
 The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
... ... 
@@ -52,9 +49,10 @@ mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
52 49 
 \seealso{
53 50 
 \itemize{
54 51 
 \item \code{matrixStats::\link[matrixStats]{rowRanges}()} and
55 
-  \code{matrixStats::\link[matrixStats]{colRanges}()} which are used when
56 
-  the input is a \code{matrix} or \code{numeric} vector.
57 
-\item For max estimates, see \code{\link{rowMaxs}()}.
58 
-\item For min estimates, see \code{\link{rowMins}()}.
52 
+\code{matrixStats::\link[matrixStats]{colRanges}()} which are used when
53 
+the input is a \code{matrix} or \code{numeric} vector.
54 
+\item For max estimates, see \code{\link[MatrixGenerics]{rowMaxs}()}.
55 
+\item For min estimates, see \code{\link[MatrixGenerics]{rowMins}()}.
56 
+\item \link{range}
59 57 
 }
60 58 
 }
Browse code

Use MatrixGenerics for other main functions:

- col/rowMaxs
- col/rowMeans2
- col/rowMedians
- col/rowMins
- col/rowRanges
- col/rowSds
- col/rowVars

const-ae authored on 13/12/2019 13:59:24
Showing 1 changed files
man/colRanges-dgCMatrix-method.Rd
History View file @ ea44315
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,60 @@
1 
+% Generated by roxygen2: do not edit by hand
2 
+% Please edit documentation in R/methods.R, R/methods_row.R
3 
+\docType{methods}
4 
+\name{colRanges,dgCMatrix-method}
5 
+\alias{colRanges,dgCMatrix-method}
6 
+\alias{rowRanges,dgCMatrix-method}
7 
+\title{Calculates the mininum and maximum for each row (column) of a matrix-like object}
8 
+\usage{
9 
+\S4method{colRanges}{dgCMatrix}(x, rows = NULL, cols = NULL,
10 
+  na.rm = FALSE, ...)
11 
+
12 
+\S4method{rowRanges}{dgCMatrix}(x, rows = NULL, cols = NULL,
13 
+  na.rm = FALSE, ...)
14 
+}
15 
+\arguments{
16 
+\item{x}{An NxK matrix-like object.}
17 
+
18 
+\item{rows}{A \code{\link[base]{vector}} indicating the subset (and/or
19 
+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
20 
+
21 
+\item{cols}{A \code{\link[base]{vector}} indicating the subset (and/or
22 
+columns) to operate over. If \code{\link[base]{NULL}}, no subsetting is done.}
23 
+
24 
+\item{na.rm}{If \code{\link[base:logical]{TRUE}}, \code{\link[base]{NA}}s
25 
+are excluded first, otherwise not.}
26 
+
27 
+\item{...}{Additional arguments passed to specific methods.}
28 
+}
29 
+\value{
30 
+a \code{\link[base]{numeric}} \code{Nx2} (\code{Kx2}) \code{\link{matrix}}, where
31 
+  N (K) is the number of rows (columns) for which the ranges are calculated.
32 
+}
33 
+\description{
34 
+Calculates the mininum and maximum for each row (column) of a matrix-like object.
35 
+}
36 
+\details{
37 
+The S4 methods for \code{x} of type \code{\link[base]{matrix}} or
38 
+\code{\link[base]{numeric}} call \code{matrixStats::\link[matrixStats]{rowRanges}}
39 
+/ \code{matrixStats::\link[matrixStats]{colRanges}}.
40 
+}
41 
+\examples{
42 
+mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
43 
+  mat[2, 1] <- NA
44 
+  mat[3, 3] <- Inf
45 
+  mat[4, 1] <- 0
46 
+
47 
+  print(mat)
48 
+
49 
+  rowRanges(mat)
50 
+  colRanges(mat)
51 
+}
52 
+\seealso{
53 
+\itemize{
54 
+\item \code{matrixStats::\link[matrixStats]{rowRanges}()} and
55 
+  \code{matrixStats::\link[matrixStats]{colRanges}()} which are used when
56 
+  the input is a \code{matrix} or \code{numeric} vector.
57 
+\item For max estimates, see \code{\link{rowMaxs}()}.
58 
+\item For min estimates, see \code{\link{rowMins}()}.
59 
+}
60 
+}