colAvgsPerRowSet: Calculates for each row (column) a summary statistic for...

In DelayedMatrixStats: Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects

Description

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

Usage

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

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

Arguments

X	A NxM DelayedMatrix.
W	An optional numeric NxM matrix of weights.
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 specific methods.
force_block_processing	FALSE (the default) means that a seed-aware, optimised method is used (if available). This can be overridden to use the general block-processing strategy by setting this to TRUE (typically not advised). The block-processing strategy loads one or more (depending on \link[DelayedArray]{getAutoBlockSize}()) columns (colFoo()) or rows (rowFoo()) into memory as an ordinary base::array.
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.
rows	A vector indicating the subset (and/or columns) to operate over. If NULL, no subsetting is done.

Details

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

Value

Returns a numeric JxN (MxJ) matrix.

Author(s)

Peter Hickey

See Also

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

Examples

# A DelayedMatrix with a 'DataFrame' seed
dm_DF <- DelayedArray(S4Vectors::DataFrame(C1 = rep(1L, 5),
                                           C2 = as.integer((0:4) ^ 2),
                                           C3 = seq(-5L, -1L, 1L)))
colAvgsPerRowSet(dm_DF, S = matrix(1:2, ncol = 2))

rowAvgsPerColSet(dm_DF, S = matrix(1:2, ncol = 1))

DelayedMatrixStats documentation built on Feb. 5, 2021, 2:04 a.m.