Package 'MatrixGenerics'

Title: S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
Description: S4 generic functions modeled after the 'matrixStats' API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities.
Authors: Constantin Ahlmann-Eltze [aut] , Peter Hickey [aut, cre] , Hervé Pagès [aut]
Maintainer: Peter Hickey <[email protected]>
License: Artistic-2.0
Version: 1.19.0
Built: 2024-11-06 05:58:16 UTC
Source: https://github.com/bioc/MatrixGenerics

Help Index

The MatrixGenerics package

Description

The MatrixGenerics package defines S4 generic summary statistic functions that operate on matrix-Like objects.

Check if all elements in a row (column) of a matrix-like object are equal to a value

Description

Check if all elements in a row (column) of a matrix-like object are equal to a value.

Usage

rowAlls(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowAlls(x, rows = NULL,
  cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
rowAlls(x, rows = NULL, cols = NULL, value = TRUE,
  na.rm = FALSE, ..., useNames = TRUE)

colAlls(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colAlls(x, rows = NULL,
  cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
colAlls(x, rows = NULL, cols = NULL, value = TRUE,
  na.rm = FALSE, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
value

The value to search for.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowAlls / matrixStats::colAlls.

Value

Returns a logical vector of length N (K).

See Also

  • matrixStats::rowAlls() and matrixStats::colAlls() which are used when the input is a matrix or numeric vector.

  • For checks if any element is equal to a value, see rowAnys().

  • base::all().

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowAlls(mat)
colAlls(mat)

Check if any elements in a row (column) of a matrix-like object is missing

Description

Check if any elements in a row (column) of a matrix-like object is missing.

Usage

rowAnyNAs(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowAnyNAs(x, rows = NULL,
  cols = NULL, ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowAnyNAs(x, rows = NULL, cols = NULL, ...,
  useNames = TRUE)

colAnyNAs(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colAnyNAs(x, rows = NULL,
  cols = NULL, ..., useNames = TRUE)

## S4 method for signature 'ANY'
colAnyNAs(x, rows = NULL, cols = NULL, ...,
  useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowAnyNAs / matrixStats::colAnyNAs.

Value

Returns a logical vector of length N (K).

See Also

  • matrixStats::rowAnyNAs() and matrixStats::colAnyNAs() which are used when the input is a matrix or numeric vector.

  • For checks if any element is equal to a value, see rowAnys().

  • base::is.na() and base::any().

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowAnyNAs(mat)
colAnyNAs(mat)

Check if any elements in a row (column) of a matrix-like object is equal to a value

Description

Check if any elements in a row (column) of a matrix-like object is equal to a value.

Usage

rowAnys(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowAnys(x, rows = NULL,
  cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
rowAnys(x, rows = NULL, cols = NULL, value = TRUE,
  na.rm = FALSE, ..., useNames = TRUE)

colAnys(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colAnys(x, rows = NULL,
  cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
colAnys(x, rows = NULL, cols = NULL, value = TRUE,
  na.rm = FALSE, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
value

The value to search for.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowAnys / matrixStats::colAnys.

Value

Returns a logical vector of length N (K).

See Also

  • matrixStats::rowAnys() and matrixStats::colAnys() which are used when the input is a matrix or numeric vector.

  • For checks if all elements are equal to a value, see rowAlls().

  • base::any().

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowAnys(mat)
colAnys(mat)

Calculates for each row (column) a summary statistic for equally sized subsets of columns (rows)

Description

Calculates for each row (column) a summary statistic for equally sized subsets of columns (rows).

Usage

rowAvgsPerColSet(X, W = NULL, rows = NULL, S, FUN = rowMeans, ...,
  na.rm = NA, tFUN = FALSE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowAvgsPerColSet(X, W = NULL,
  rows = NULL, S, FUN = rowMeans, ..., na.rm = NA, tFUN = FALSE)

## S4 method for signature 'ANY'
rowAvgsPerColSet(X, W = NULL, rows = NULL, S,
  FUN = rowMeans, ..., na.rm = NA, tFUN = FALSE)

colAvgsPerRowSet(X, W = NULL, cols = NULL, S, FUN = colMeans, ...,
  na.rm = NA, tFUN = FALSE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colAvgsPerRowSet(X, W = NULL,
  cols = NULL, S, FUN = colMeans, ..., na.rm = NA, tFUN = FALSE)

## S4 method for signature 'ANY'
colAvgsPerRowSet(X, W = NULL, cols = NULL, S,
  FUN = colMeans, ..., na.rm = NA, tFUN = FALSE)

Arguments

X

An NxM matrix-like object.
W

An optional numeric NxM matrix of weights.
rows, cols

A vector indicating the subset (and/or columns) to operate over. If NULL, no subsetting is done.
S

An integer KxJ matrix that specifying the J subsets. Each column hold K column (row) indices for the corresponding subset. The range of values is [1, M] ([1,N]).
FUN

A row-by-row (column-by-column) summary statistic function. It is applied to to each column (row) subset of X that is specified by S.
...

Additional arguments passed to FUN.
na.rm

(logical) Argument passed to FUN() as na.rm = na.rm. If NA (default), then na.rm = TRUE is used if X or S holds missing values, otherwise na.rm = FALSE.
tFUN

If TRUE, X is transposed before it is passed to FUN.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowAvgsPerColSet / matrixStats::colAvgsPerRowSet.

Value

Returns a numeric JxN (MxJ) matrix.

See Also

Examples

mat <- matrix(rnorm(20), nrow = 5, ncol = 4)
  mat[2, 1] <- NA
  mat[3, 3] <- Inf
  mat[4, 1] <- 0
  
  print(mat)
  
  S <- matrix(1:ncol(mat), ncol = 2)
  print(S)
  
  rowAvgsPerColSet(mat, S = S, FUN = rowMeans)
  rowAvgsPerColSet(mat, S = S, FUN = rowVars)

Extract one cell from each row (column) of a matrix-like object

Description

Extract one cell from each row (column) of a matrix-like object.

Usage

rowCollapse(x, idxs, rows = NULL, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowCollapse(x, idxs,
  rows = NULL, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowCollapse(x, idxs, rows = NULL, ..., useNames = TRUE)

colCollapse(x, idxs, cols = NULL, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colCollapse(x, idxs,
  cols = NULL, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
colCollapse(x, idxs, cols = NULL, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
idxs

An index vector with the position to extract. It is recycled to match the number of rows (column)
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowCollapse / matrixStats::colCollapse.

Value

Returns a numeric vector of length N (K).

See Also

  • matrixStats::rowCollapse() and matrixStats::colCollapse() which are used when the input is a matrix or numeric vector.

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
  mat[2, 1] <- NA
  mat[3, 3] <- Inf
  mat[4, 1] <- 0

  print(mat)

  rowCollapse(mat, idxs = 2)
  rowCollapse(mat, idxs = c(1,1,2,3,2))

  colCollapse (mat, idxs = 4)

Count how often an element in a row (column) of a matrix-like object is equal to a value

Description

Count how often an element in a row (column) of a matrix-like object is equal to a value.

Usage

rowCounts(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
  ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowCounts(x, rows = NULL,
  cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
rowCounts(x, rows = NULL, cols = NULL, value = TRUE,
  na.rm = FALSE, ..., useNames = TRUE)

colCounts(x, rows = NULL, cols = NULL, value = TRUE, na.rm = FALSE,
  ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colCounts(x, rows = NULL,
  cols = NULL, value = TRUE, na.rm = FALSE, dim. = dim(x), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
colCounts(x, rows = NULL, cols = NULL, value = TRUE,
  na.rm = FALSE, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
value

The value to search for.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowCounts / matrixStats::colCounts.

Value

Returns a integer vector of length N (K).

See Also

  • matrixStats::rowCounts() and matrixStats::colCounts() which are used when the input is a matrix or numeric vector.

  • For checks if any element is equal to a value, see rowAnys(). To check if all elements are equal, see rowAlls().

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowCounts(mat)
colCounts(mat)
  rowCounts(mat, value = 0)
  colCounts(mat, value = Inf, na.rm = TRUE)

Calculates the cumulative maxima for each row (column) of a matrix-like object

Description

Calculates the cumulative maxima for each row (column) of a matrix-like object.

Usage

rowCummaxs(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowCummaxs(x, rows = NULL,
  cols = NULL, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowCummaxs(x, rows = NULL, cols = NULL, ...,
  useNames = TRUE)

colCummaxs(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colCummaxs(x, rows = NULL,
  cols = NULL, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
colCummaxs(x, rows = NULL, cols = NULL, ...,
  useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowCummaxs / matrixStats::colCummaxs.

Value

Returns a numeric matrixwith the same dimensions as x.

See Also

  • matrixStats::rowCummaxs() and matrixStats::colCummaxs() which are used when the input is a matrix or numeric vector.

  • For single maximum estimates, see rowMaxs().

  • base::cummax().

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowCummaxs(mat)
colCummaxs(mat)

Calculates the cumulative minima for each row (column) of a matrix-like object

Description

Calculates the cumulative minima for each row (column) of a matrix-like object.

Usage

rowCummins(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowCummins(x, rows = NULL,
  cols = NULL, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowCummins(x, rows = NULL, cols = NULL, ...,
  useNames = TRUE)

colCummins(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colCummins(x, rows = NULL,
  cols = NULL, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
colCummins(x, rows = NULL, cols = NULL, ...,
  useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowCummins / matrixStats::colCummins.

Value

Returns a numeric matrixwith the same dimensions as x.

See Also

  • matrixStats::rowCummins() and matrixStats::colCummins() which are used when the input is a matrix or numeric vector.

  • For single minimum estimates, see rowMins().

  • base::cummin().

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowCummins(mat)
colCummins(mat)

Calculates the cumulative product for each row (column) of a matrix-like object

Description

Calculates the cumulative product for each row (column) of a matrix-like object.

Usage

rowCumprods(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowCumprods(x, rows = NULL,
  cols = NULL, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowCumprods(x, rows = NULL, cols = NULL, ...,
  useNames = TRUE)

colCumprods(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colCumprods(x, rows = NULL,
  cols = NULL, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
colCumprods(x, rows = NULL, cols = NULL, ...,
  useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowCumprods / matrixStats::colCumprods.

Value

Returns a numeric matrixwith the same dimensions as x.

See Also

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowCumprods(mat)
colCumprods(mat)

Calculates the cumulative sum for each row (column) of a matrix-like object

Description

Calculates the cumulative sum for each row (column) of a matrix-like object.

Usage

rowCumsums(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowCumsums(x, rows = NULL,
  cols = NULL, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowCumsums(x, rows = NULL, cols = NULL, ...,
  useNames = TRUE)

colCumsums(x, rows = NULL, cols = NULL, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colCumsums(x, rows = NULL,
  cols = NULL, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
colCumsums(x, rows = NULL, cols = NULL, ...,
  useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowCumsums / matrixStats::colCumsums.

Value

Returns a numeric matrixwith the same dimensions as x.

See Also

  • matrixStats::rowCumsums() and matrixStats::colCumsums() which are used when the input is a matrix or numeric vector.

  • base::cumsum().

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowCumsums(mat)
colCumsums(mat)

Calculates the difference between each element of a row (column) of a matrix-like object

Description

Calculates the difference between each element of a row (column) of a matrix-like object.

Usage

rowDiffs(x, rows = NULL, cols = NULL, lag = 1L, differences = 1L, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowDiffs(x, rows = NULL,
  cols = NULL, lag = 1L, differences = 1L, dim. = dim(x), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
rowDiffs(x, rows = NULL, cols = NULL, lag = 1L,
  differences = 1L, ..., useNames = TRUE)

colDiffs(x, rows = NULL, cols = NULL, lag = 1L, differences = 1L, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colDiffs(x, rows = NULL,
  cols = NULL, lag = 1L, differences = 1L, dim. = dim(x), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
colDiffs(x, rows = NULL, cols = NULL, lag = 1L,
  differences = 1L, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
lag

An integer specifying the lag.
differences

An integer specifying the order of difference.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowDiffs / matrixStats::colDiffs.

Value

Returns a numeric matrix with one column (row) less than x: Nx(K−1)Nx(K-1) or (N−1)xK(N-1)xK.

See Also

  • matrixStats::rowDiffs() and matrixStats::colDiffs() which are used when the input is a matrix or numeric vector.

  • base::diff().

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowDiffs(mat)
colDiffs(mat)

Calculates the interquartile range of the difference between each element of a row (column) of a matrix-like object

Description

Calculates the interquartile range of the difference between each element of a row (column) of a matrix-like object.

Usage

rowIQRDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowIQRDiffs(x, rows = NULL,
  cols = NULL, na.rm = FALSE, diff = 1L, trim = 0, ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
rowIQRDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE,
  diff = 1L, trim = 0, ..., useNames = TRUE)

colIQRDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colIQRDiffs(x, rows = NULL,
  cols = NULL, na.rm = FALSE, diff = 1L, trim = 0, ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
colIQRDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE,
  diff = 1L, trim = 0, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
diff

An integer specifying the order of difference.
trim

A double in [0,1/2] specifying the fraction of observations to be trimmed from each end of (sorted) x before estimation.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowIQRDiffs / matrixStats::colIQRDiffs.

Value

Returns a numeric vector of length N (K).

See Also

  • matrixStats::rowIQRDiffs() and matrixStats::colIQRDiffs() which are used when the input is a matrix or numeric vector.

  • For the direct interquartile range see also rowIQRs.

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowIQRDiffs(mat)
colIQRDiffs(mat)

Calculates the interquartile range for each row (column) of a matrix-like object

Description

Calculates the interquartile range for each row (column) of a matrix-like object.

Usage

rowIQRs(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowIQRs(x, rows = NULL,
  cols = NULL, na.rm = FALSE, ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowIQRs(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

colIQRs(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colIQRs(x, rows = NULL,
  cols = NULL, na.rm = FALSE, ..., useNames = TRUE)

## S4 method for signature 'ANY'
colIQRs(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowIQRs / matrixStats::colIQRs.

Value

Returns a numeric vector of length N (K).

See Also

  • matrixStats::rowIQRs() and matrixStats::colIQRs() which are used when the input is a matrix or numeric vector.

  • For a non-robust analog, see rowSds(). For a more robust version see rowMads()

  • stats::IQR().

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowIQRs(mat)
colIQRs(mat)

Accurately calculates the logarithm of the sum of exponentials for each row (column) of a matrix-like object

Description

Accurately calculates the logarithm of the sum of exponentials for each row (column) of a matrix-like object.

Usage

rowLogSumExps(lx, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowLogSumExps(lx,
  rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(lx), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
rowLogSumExps(lx, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)

colLogSumExps(lx, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colLogSumExps(lx,
  rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(lx), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
colLogSumExps(lx, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)

Arguments

lx

An NxK matrix-like object. Typically lx are log(x) values.
rows, cols

A vector indicating the subset (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowLogSumExps / matrixStats::colLogSumExps.

Value

Returns a numeric vector of length N (K).

See Also

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowLogSumExps(mat)
colLogSumExps(mat)

Calculates the mean absolute deviation of the difference between each element of a row (column) of a matrix-like object

Description

Calculates the mean absolute deviation of the difference between each element of a row (column) of a matrix-like object.

Usage

rowMadDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowMadDiffs(x, rows = NULL,
  cols = NULL, na.rm = FALSE, diff = 1L, trim = 0, ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
rowMadDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE,
  diff = 1L, trim = 0, ..., useNames = TRUE)

colMadDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colMadDiffs(x, rows = NULL,
  cols = NULL, na.rm = FALSE, diff = 1L, trim = 0, ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
colMadDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE,
  diff = 1L, trim = 0, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
diff

An integer specifying the order of difference.
trim

A double in [0,1/2] specifying the fraction of observations to be trimmed from each end of (sorted) x before estimation.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowMadDiffs / matrixStats::colMadDiffs.

Value

Returns a numeric vector of length N (K).

See Also

  • matrixStats::rowMadDiffs() and matrixStats::colMadDiffs() which are used when the input is a matrix or numeric vector.

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowMadDiffs(mat)
colMadDiffs(mat)

Calculates the median absolute deviation for each row (column) of a matrix-like object

Description

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

Usage

rowMads(x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826,
  na.rm = FALSE, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowMads(x, rows = NULL,
  cols = NULL, center = NULL, constant = 1.4826, na.rm = FALSE,
  dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowMads(x, rows = NULL, cols = NULL, center = NULL,
  constant = 1.4826, na.rm = FALSE, ..., useNames = TRUE)

colMads(x, rows = NULL, cols = NULL, center = NULL, constant = 1.4826,
  na.rm = FALSE, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colMads(x, rows = NULL,
  cols = NULL, center = NULL, constant = 1.4826, na.rm = FALSE,
  dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
colMads(x, rows = NULL, cols = NULL, center = NULL,
  constant = 1.4826, na.rm = FALSE, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
center

(optional) the center, defaults to the row means
constant

A scale factor. See stats::mad() for details.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowMads / matrixStats::colMads.

Value

Returns a numeric vector of length N (K).

See Also

  • matrixStats::rowMads() and matrixStats::colMads() which are used when the input is a matrix or numeric vector.

  • For mean estimates, see rowMeans2() and rowMeans().

  • For non-robust standard deviation estimates, see rowSds().

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowMads(mat)
colMads(mat)

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

Description

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

Usage

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

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowMaxs(x, rows = NULL,
  cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowMaxs(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

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

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colMaxs(x, rows = NULL,
  cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
colMaxs(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowMaxs / matrixStats::colMaxs.

Value

Returns a numeric vector of length N (K).

See Also

  • matrixStats::rowMaxs() and matrixStats::colMaxs() which are used when the input is a matrix or numeric vector.

  • For min estimates, see rowMins().

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)

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

Description

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

Usage

rowMeans(x, na.rm = FALSE, dims = 1, ...)

colMeans(x, na.rm = FALSE, dims = 1, ...)

Arguments

x

An NxK matrix-like object, a numeric data frame, or an array-like object of two or more dimensions.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
dims

A single integer indicating which dimensions are regarded as rows or columns to mean over. For rowMeans, the mean is over dimensions dims+1, ...; for colMeans it is over dimensions 1:dims.
...

Additional arguments passed to specific methods.

Details

This man page documents the rowMeans and colMeans S4 generic functions defined in the MatrixGenerics package. See ?base::colMeans for the default methods (defined in the base package).

Value

Returns a numeric vector of length N (K).

See Also

  • base::colMeans for the default rowMeans and colMeans methods.

  • Matrix::colMeans in the Matrix package for rowMeans and colMeans methods defined for CsparseMatrix derivatives (e.g. dgCMatrix objects).

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowMeans(mat)
colMeans(mat)

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

Description

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

Usage

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

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowMeans2(x, rows = NULL,
  cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowMeans2(x, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

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

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colMeans2(x, rows = NULL,
  cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
colMeans2(x, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowMeans2 / matrixStats::colMeans2.

Value

Returns a numeric vector of length N (K).

See Also

  • matrixStats::rowMeans2() and matrixStats::colMeans2() which are used when the input is a matrix or numeric vector.

  • See also rowMeans() for the corresponding function in base R.

  • For variance estimates, see rowVars().

  • See also the base R version base::rowMeans().

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)

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

Description

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

Usage

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

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowMedians(x, rows = NULL,
  cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowMedians(x, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

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

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colMedians(x, rows = NULL,
  cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
colMedians(x, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowMedians / matrixStats::colMedians.

Value

Returns a numeric vector of length N (K).

See Also

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)

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

Description

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

Usage

rowMins(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowMins(x, rows = NULL,
  cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowMins(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

colMins(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colMins(x, rows = NULL,
  cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
colMins(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowMins / matrixStats::colMins.

Value

Returns a numeric vector of length N (K).

See Also

  • matrixStats::rowMins() and matrixStats::colMins() which are used when the input is a matrix or numeric vector.

  • For max estimates, see rowMaxs().

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)

Calculates an order statistic for each row (column) of a matrix-like object

Description

Calculates an order statistic for each row (column) of a matrix-like object.

Usage

rowOrderStats(x, rows = NULL, cols = NULL, which, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowOrderStats(x, rows = NULL,
  cols = NULL, which, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowOrderStats(x, rows = NULL, cols = NULL, which, ...,
  useNames = TRUE)

colOrderStats(x, rows = NULL, cols = NULL, which, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colOrderStats(x, rows = NULL,
  cols = NULL, which, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
colOrderStats(x, rows = NULL, cols = NULL, which, ...,
  useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
which

An integer index in [1,K] ([1,N]) indicating which order statistic to be returned
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowOrderStats / matrixStats::colOrderStats.

Value

Returns a numeric vector of length N (K).

See Also

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
    mat[2, 1] <- 2
    mat[3, 3] <- Inf
    mat[4, 1] <- 0

    print(mat)

    rowOrderStats(mat, which = 1)
    colOrderStats(mat, which = 3)

Calculates the product for each row (column) of a matrix-like object

Description

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

Usage

rowProds(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowProds(x, rows = NULL,
  cols = NULL, na.rm = FALSE, method = c("direct", "expSumLog"), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
rowProds(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

colProds(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colProds(x, rows = NULL,
  cols = NULL, na.rm = FALSE, method = c("direct", "expSumLog"), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
colProds(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
method

A character vector of length one that specifies the how the product is calculated. Note, that this is not a generic argument and not all implementation have to provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowProds / matrixStats::colProds.

Value

Returns a numeric vector of length N (K).

See Also

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowProds(mat)
colProds(mat)

Calculates quantiles for each row (column) of a matrix-like object

Description

Calculates quantiles for each row (column) of a matrix-like object.

Usage

rowQuantiles(x, rows = NULL, cols = NULL, probs = seq(from = 0, to = 1,
  by = 0.25), na.rm = FALSE, type = 7L, digits = 7L, ...,
  useNames = TRUE, drop = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowQuantiles(x, rows = NULL,
  cols = NULL, probs = seq(from = 0, to = 1, by = 0.25), na.rm = FALSE,
  type = 7L, digits = 7L, ..., useNames = TRUE, drop = TRUE)

## S4 method for signature 'ANY'
rowQuantiles(x, rows = NULL, cols = NULL,
  probs = seq(from = 0, to = 1, by = 0.25), na.rm = FALSE, type = 7L,
  digits = 7L, ..., useNames = TRUE, drop = TRUE)

colQuantiles(x, rows = NULL, cols = NULL, probs = seq(from = 0, to = 1,
  by = 0.25), na.rm = FALSE, type = 7L, digits = 7L, ...,
  useNames = TRUE, drop = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colQuantiles(x, rows = NULL,
  cols = NULL, probs = seq(from = 0, to = 1, by = 0.25), na.rm = FALSE,
  type = 7L, digits = 7L, ..., useNames = TRUE, drop = TRUE)

## S4 method for signature 'ANY'
colQuantiles(x, rows = NULL, cols = NULL,
  probs = seq(from = 0, to = 1, by = 0.25), na.rm = FALSE, type = 7L,
  digits = 7L, ..., useNames = TRUE, drop = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
probs

A numeric vector of J probabilities in [0, 1].
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
type

An integer specifying the type of estimator. See stats::quantile() for more details.
digits

An integer specifying the precision of the formatted percentages. See stats::quantile() for more details.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
drop

If TRUE a vector is returned if J == 1.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowQuantiles / matrixStats::colQuantiles.

Value

a numeric NxJ (KxJ) matrix, where N (K) is the number of rows (columns) for which the J values are calculated.

See Also

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowQuantiles(mat)
colQuantiles(mat)

Calculates the minimum and maximum for each row (column) of a matrix-like object

Description

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

Usage

rowRanges(x, ...)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowRanges(x, rows = NULL,
  cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowRanges(x, ...)

colRanges(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colRanges(x, rows = NULL,
  cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
colRanges(x, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
...

Additional arguments passed to specific methods.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowRanges / matrixStats::colRanges.

Value

a numeric Nx2 (Kx2) matrix, where N (K) is the number of rows (columns) for which the ranges are calculated.

Note

Unfortunately for the argument list of the rowRanges() generic function we cannot follow the scheme used for the other row/column matrix summarization generic functions. This is because we need to be compatible with the historic rowRanges() getter for RangedSummarizedExperiment objects. See ?SummarizedExperiment::rowRanges.

See Also

  • matrixStats::rowRanges() and matrixStats::colRanges() which are used when the input is a matrix or numeric vector.

  • For max estimates, see rowMaxs().

  • For min estimates, see rowMins().

  • base::range().

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowRanges(mat)
colRanges(mat)

Calculates the rank of the elements for each row (column) of a matrix-like object

Description

Calculates the rank of the elements for each row (column) of a matrix-like object.

Usage

rowRanks(x, rows = NULL, cols = NULL, ties.method = c("max", "average"),
  ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowRanks(x, rows = NULL,
  cols = NULL, ties.method = c("max", "average", "first", "last", "random",
  "max", "min", "dense"), dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowRanks(x, rows = NULL, cols = NULL,
  ties.method = c("max", "average"), ..., useNames = TRUE)

colRanks(x, rows = NULL, cols = NULL, ties.method = c("max", "average"),
  ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colRanks(x, rows = NULL,
  cols = NULL, ties.method = c("max", "average", "first", "last", "random",
  "max", "min", "dense"), dim. = dim(x), preserveShape = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
colRanks(x, rows = NULL, cols = NULL,
  ties.method = c("max", "average"), ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
ties.method

A character string specifying how ties are treated. Note that the default specifies fewer options than the original matrixStats package.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.
preserveShape

If TRUE the output matrix has the same shape as the input x. Note, that this is not a generic argument and not all implementation of this function have to provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowRanks / matrixStats::colRanks.

The matrixStats::rowRanks() function can handle a lot of different values for the ties.method argument. Users of the generic function should however only rely on max and average because the other ones are not guaranteed to be implemented:

max

for values with identical values the maximum rank is returned

average

for values with identical values the average of the ranks they cover is returned. Note, that in this case the return value is of type numeric.

Value

a matrix of type integer is returned unless ties.method = "average". Ithas dimensions' NxJ (KxJ) matrix, where N (K) is the number of rows (columns) of the input x.

See Also

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowRanks(mat)
colRanks(mat)

Calculates the standard deviation of the difference between each element of a row (column) of a matrix-like object

Description

Calculates the standard deviation of the difference between each element of a row (column) of a matrix-like object.

Usage

rowSdDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowSdDiffs(x, rows = NULL,
  cols = NULL, na.rm = FALSE, diff = 1L, trim = 0, ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
rowSdDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE,
  diff = 1L, trim = 0, ..., useNames = TRUE)

colSdDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colSdDiffs(x, rows = NULL,
  cols = NULL, na.rm = FALSE, diff = 1L, trim = 0, ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
colSdDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE,
  diff = 1L, trim = 0, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
diff

An integer specifying the order of difference.
trim

A double in [0,1/2] specifying the fraction of observations to be trimmed from each end of (sorted) x before estimation.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowSdDiffs / matrixStats::colSdDiffs.

Value

Returns a numeric vector of length N (K).

See Also

  • matrixStats::rowSdDiffs() and matrixStats::colSdDiffs() which are used when the input is a matrix or numeric vector.

  • for the direct standard deviation see rowSds().

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowSdDiffs(mat)
colSdDiffs(mat)

Calculates the standard deviation for each row (column) of a matrix-like object

Description

Calculates the standard deviation for each row (column) of a matrix-like object.

Usage

rowSds(x, rows = NULL, cols = NULL, na.rm = FALSE, center = NULL, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowSds(x, rows = NULL,
  cols = NULL, na.rm = FALSE, center = NULL, dim. = dim(x), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
rowSds(x, rows = NULL, cols = NULL, na.rm = FALSE,
  center = NULL, ..., useNames = TRUE)

colSds(x, rows = NULL, cols = NULL, na.rm = FALSE, center = NULL, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colSds(x, rows = NULL,
  cols = NULL, na.rm = FALSE, center = NULL, dim. = dim(x), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
colSds(x, rows = NULL, cols = NULL, na.rm = FALSE,
  center = NULL, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
center

(optional) the center, defaults to the row means
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowSds / matrixStats::colSds.

Value

Returns a numeric vector of length N (K).

See Also

  • matrixStats::rowSds() and matrixStats::colSds() which are used when the input is a matrix or numeric vector.

  • For mean estimates, see rowMeans2() and rowMeans().

  • For variance estimates, see rowVars().

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowSds(mat)
colSds(mat)

Calculates the sum for each row (column) of a matrix-like object

Description

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

Usage

rowSums(x, na.rm = FALSE, dims = 1, ...)

colSums(x, na.rm = FALSE, dims = 1, ...)

Arguments

x

An NxK matrix-like object, a numeric data frame, or an array-like object of two or more dimensions.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
dims

A single integer indicating which dimensions are regarded as rows or columns to sum over. For rowSums, the sum is over dimensions dims+1, ...; for colSums it is over dimensions 1:dims.
...

Additional arguments passed to specific methods.

Details

This man page documents the rowSums and colSums S4 generic functions defined in the MatrixGenerics package. See ?base::colSums for the default methods (defined in the base package).

Value

Returns a numeric vector of length N (K).

See Also

  • base::colSums for the default rowSums and colSums methods.

  • Matrix::colSums in the Matrix package for rowSums and colSums methods defined for CsparseMatrix derivatives (e.g. dgCMatrix objects).

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowSums(mat)
colSums(mat)

Calculates the sum for each row (column) of a matrix-like object

Description

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

Usage

rowSums2(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowSums2(x, rows = NULL,
  cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowSums2(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

colSums2(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colSums2(x, rows = NULL,
  cols = NULL, na.rm = FALSE, dim. = dim(x), ..., useNames = TRUE)

## S4 method for signature 'ANY'
colSums2(x, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowSums2 / matrixStats::colSums2.

Value

Returns a numeric vector of length N (K).

See Also

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowSums2(mat)
colSums2(mat)

Tabulates the values in a matrix-like object by row (column)

Description

Tabulates the values in a matrix-like object by row (column).

Usage

rowTabulates(x, rows = NULL, cols = NULL, values = NULL, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowTabulates(x, rows = NULL,
  cols = NULL, values = NULL, ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowTabulates(x, rows = NULL, cols = NULL, values = NULL,
  ..., useNames = TRUE)

colTabulates(x, rows = NULL, cols = NULL, values = NULL, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colTabulates(x, rows = NULL,
  cols = NULL, values = NULL, ..., useNames = TRUE)

## S4 method for signature 'ANY'
colTabulates(x, rows = NULL, cols = NULL, values = NULL,
  ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
values

the values to search for.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowTabulates / matrixStats::colTabulates.

Value

a numeric NxJ (KxJ) matrix, where N (K) is the number of rows (columns) for which the J values are calculated.

See Also

Examples

mat <- matrix(rpois(15, lambda = 3), nrow = 5, ncol = 3)
  mat[2, 1] <- NA_integer_
  mat[3, 3] <- 0L
  mat[4, 1] <- 0L

  print(mat)

  rowTabulates(mat)
  colTabulates(mat)

  rowTabulates(mat, values = 0)
  colTabulates(mat, values = 0)

Calculates the variance of the difference between each element of a row (column) of a matrix-like object

Description

Calculates the variance of the difference between each element of a row (column) of a matrix-like object.

Usage

rowVarDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowVarDiffs(x, rows = NULL,
  cols = NULL, na.rm = FALSE, diff = 1L, trim = 0, ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
rowVarDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE,
  diff = 1L, trim = 0, ..., useNames = TRUE)

colVarDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE, diff = 1L,
  trim = 0, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colVarDiffs(x, rows = NULL,
  cols = NULL, na.rm = FALSE, diff = 1L, trim = 0, ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
colVarDiffs(x, rows = NULL, cols = NULL, na.rm = FALSE,
  diff = 1L, trim = 0, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
diff

An integer specifying the order of difference.
trim

A double in [0,1/2] specifying the fraction of observations to be trimmed from each end of (sorted) x before estimation.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowVarDiffs / matrixStats::colVarDiffs.

Value

Returns a numeric vector of length N (K).

See Also

  • matrixStats::rowVarDiffs() and matrixStats::colVarDiffs() which are used when the input is a matrix or numeric vector.

  • for the direct variance see rowVars().

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowVarDiffs(mat)
colVarDiffs(mat)

Calculates the variance for each row (column) of a matrix-like object

Description

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

Usage

rowVars(x, rows = NULL, cols = NULL, na.rm = FALSE, center = NULL, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowVars(x, rows = NULL,
  cols = NULL, na.rm = FALSE, center = NULL, dim. = dim(x), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
rowVars(x, rows = NULL, cols = NULL, na.rm = FALSE,
  center = NULL, ..., useNames = TRUE)

colVars(x, rows = NULL, cols = NULL, na.rm = FALSE, center = NULL, ...,
  useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colVars(x, rows = NULL,
  cols = NULL, na.rm = FALSE, center = NULL, dim. = dim(x), ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
colVars(x, rows = NULL, cols = NULL, na.rm = FALSE,
  center = NULL, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
center

(optional) the center, defaults to the row means.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.
dim.

An integer vector of length two specifying the dimension of x, essential when x is a numeric vector. Note, that this is not a generic argument and not all methods need provide it.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowVars / matrixStats::colVars.

Value

Returns a numeric vector of length N (K).

See Also

  • matrixStats::rowVars() and matrixStats::colVars() which are used when the input is a matrix or numeric vector.

  • For mean estimates, see rowMeans2() and rowMeans().

  • For standard deviation estimates, see rowSds().

  • stats::var().

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)

rowVars(mat)
colVars(mat)

Calculates the weighted median absolute deviation for each row (column) of a matrix-like object

Description

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

Usage

rowWeightedMads(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  constant = 1.4826, center = NULL, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowWeightedMads(x, w = NULL,
  rows = NULL, cols = NULL, na.rm = FALSE, constant = 1.4826,
  center = NULL, ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowWeightedMads(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, constant = 1.4826, center = NULL, ...,
  useNames = TRUE)

colWeightedMads(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  constant = 1.4826, center = NULL, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colWeightedMads(x, w = NULL,
  rows = NULL, cols = NULL, na.rm = FALSE, constant = 1.4826,
  center = NULL, ..., useNames = TRUE)

## S4 method for signature 'ANY'
colWeightedMads(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, constant = 1.4826, center = NULL, ...,
  useNames = TRUE)

Arguments

x

An NxK matrix-like object.
w

A numeric vector of length K (N) that specifies by how much each element is weighted.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
constant

A scale factor. See stats::mad() for details.
center

(optional) the center, defaults to the row means
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowWeightedMads / matrixStats::colWeightedMads.

Value

Returns a numeric vector of length N (K).

See Also

  • matrixStats::rowWeightedMads() and matrixStats::colWeightedMads() which are used when the input is a matrix or numeric vector.

  • See also rowMads for the corresponding unweighted function.

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)
w <- rnorm(n = 5, mean = 3)
rowWeightedMads(mat, w = w[1:3])
colWeightedMads(mat, w = w)

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

Description

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

Usage

rowWeightedMeans(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowWeightedMeans(x, w = NULL,
  rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowWeightedMeans(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)

colWeightedMeans(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colWeightedMeans(x, w = NULL,
  rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE)

## S4 method for signature 'ANY'
colWeightedMeans(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
w

A numeric vector of length K (N) that specifies by how much each element is weighted.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowWeightedMeans / matrixStats::colWeightedMeans.

Value

Returns a numeric vector of length N (K).

See Also

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)
w <- rnorm(n = 5, mean = 3)
rowWeightedMeans(mat, w = w[1:3])
colWeightedMeans(mat, w = w)

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

Description

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

Usage

rowWeightedMedians(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowWeightedMedians(x,
  w = NULL, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
rowWeightedMedians(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)

colWeightedMedians(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colWeightedMedians(x,
  w = NULL, rows = NULL, cols = NULL, na.rm = FALSE, ...,
  useNames = TRUE)

## S4 method for signature 'ANY'
colWeightedMedians(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
w

A numeric vector of length K (N) that specifies by how much each element is weighted.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowWeightedMedians / matrixStats::colWeightedMedians.

Value

Returns a numeric vector of length N (K).

See Also

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)
w <- rnorm(n = 5, mean = 3)
rowWeightedMedians(mat, w = w[1:3])
colWeightedMedians(mat, w = w)

Calculates the weighted standard deviation for each row (column) of a matrix-like object

Description

Calculates the weighted standard deviation for each row (column) of a matrix-like object.

Usage

rowWeightedSds(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowWeightedSds(x, w = NULL,
  rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowWeightedSds(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)

colWeightedSds(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colWeightedSds(x, w = NULL,
  rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE)

## S4 method for signature 'ANY'
colWeightedSds(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
w

A numeric vector of length K (N) that specifies by how much each element is weighted.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowWeightedSds / matrixStats::colWeightedSds.

Value

Returns a numeric vector of length N (K).

See Also

  • matrixStats::rowWeightedSds() and matrixStats::colWeightedSds() which are used when the input is a matrix or numeric vector.

  • See also rowSds for the corresponding unweighted function.

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)
w <- rnorm(n = 5, mean = 3)
rowWeightedSds(mat, w = w[1:3])
colWeightedSds(mat, w = w)

Calculates the weighted variance for each row (column) of a matrix-like object

Description

Calculates the weighted variance for each row (column) of a matrix-like object.

Usage

rowWeightedVars(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
rowWeightedVars(x, w = NULL,
  rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE)

## S4 method for signature 'ANY'
rowWeightedVars(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)

colWeightedVars(x, w = NULL, rows = NULL, cols = NULL, na.rm = FALSE,
  ..., useNames = TRUE)

## S4 method for signature 'matrix_OR_array_OR_table_OR_numeric'
colWeightedVars(x, w = NULL,
  rows = NULL, cols = NULL, na.rm = FALSE, ..., useNames = TRUE)

## S4 method for signature 'ANY'
colWeightedVars(x, w = NULL, rows = NULL, cols = NULL,
  na.rm = FALSE, ..., useNames = TRUE)

Arguments

x

An NxK matrix-like object.
w

A numeric vector of length K (N) that specifies by how much each element is weighted.
rows, cols

A vector indicating the subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.
na.rm

If TRUE, missing values (NA or NaN) are omitted from the calculations.
...

Additional arguments passed to specific methods.
useNames

If TRUE (default), names attributes of result are set. Else if FALSE, no naming support is done.

Details

The S4 methods for x of type matrix, array, table, or numeric call matrixStats::rowWeightedVars / matrixStats::colWeightedVars.

Value

Returns a numeric vector of length N (K).

See Also

  • matrixStats::rowWeightedVars() and matrixStats::colWeightedVars() which are used when the input is a matrix or numeric vector.

  • See also rowVars for the corresponding unweighted function.

Examples

mat <- matrix(rnorm(15), nrow = 5, ncol = 3)
mat[2, 1] <- NA
mat[3, 3] <- Inf
mat[4, 1] <- 0

print(mat)
w <- rnorm(n = 5, mean = 3)
rowWeightedVars(mat, w = w[1:3])
colWeightedVars(mat, w = w)