rowStats: Row and Column Summary Statistics Based on Grouping

In kuwisdelu/matter: Scientific computing for out-of-memory signals and images

Row and Column Summary Statistics Based on Grouping

Description

These functions perform calculation of summary statistics over matrix rows and columns for each level of a grouping variable.

Usage

## S4 method for signature 'ANY'
rowStats(x, stat, ..., BPPARAM = bpparam())

## S4 method for signature 'ANY'
colStats(x, stat, ..., BPPARAM = bpparam())

## S4 method for signature 'matter_mat'
rowStats(x, stat, ..., BPPARAM = bpparam())

## S4 method for signature 'matter_mat'
colStats(x, stat, ..., BPPARAM = bpparam())

## S4 method for signature 'sparse_mat'
rowStats(x, stat, ..., BPPARAM = bpparam())

## S4 method for signature 'sparse_mat'
colStats(x, stat, ..., BPPARAM = bpparam())

.rowStats(x, stat, group = NULL,
    na.rm = FALSE, simplify = TRUE, drop = TRUE,
    iter.dim = 1L, BPPARAM = bpparam(), ...)

.colStats(x, stat, group = NULL,
    na.rm = FALSE, simplify = TRUE, drop = TRUE,
    iter.dim = 2L, BPPARAM = bpparam(), ...)

Arguments

x	A matrix on which to calculate summary statistics.
stat	The name of summary statistics to compute over the rows or columns of a matrix. Allowable values include: "min", "max", "prod", "sum", "mean", "var", "sd", "any", "all", and "nnzero".
group	A factor or vector giving the grouping. If not provided, no grouping will be used.
na.rm	If TRUE, remove NA values before summarizing.
simplify	Simplify the results from a list to a vector or array. This also drops any additional attributes (besides names).
drop	If only a single summary statistic is calculated, return the results as a vector (or matrix) rather than a list.
iter.dim	The dimension to iterate over. Must be 1 or 2, where 1 indicates rows and 2 indicates columns.
BPPARAM	An optional instance of BiocParallelParam. See documentation for bplapply.
...	Additional arguments passed to chunk_rowapply() or chunk_colapply(), such as the number of chunks.

Details

The summary statistics methods are calculated over chunks of the matrix using s_colstats and s_rowstats. For matter objects, the iteration is performed over the major dimension for IO efficiency.

Value

A list for each stat requested, where each element is either a vector (if no grouping variable is provided) or a matrix where each column corresponds to a different level of group.

If drop=TRUE, and only a single statistic is requested, then the result will be unlisted and returned as a vector or matrix.

Author(s)

Kylie A. Bemis

See Also

colSums

Examples

register(SerialParam())

set.seed(1)

x <- matrix(runif(100^2), nrow=100, ncol=100)

g <- as.factor(rep(letters[1:5], each=20))

colStats(x, "mean", group=g)

kuwisdelu/matter documentation built on May 11, 2024, 9:15 a.m.