R: Give Column and Row Sums of an _HDF5Matrix

colsum,HDF5Matrix-method {DelayedMatrixStats}

R Documentation

Give Column and Row Sums of an HDF5Matrix Based on a Grouping Variable

Description

Compute column and row sums across rows or columns of a numeric HDF5Array::HDF5Matrix object for each level of a grouping variable.

Usage

## S4 method for signature 'HDF5Matrix'
colsum(x, group, reorder = TRUE, na.rm = FALSE,
  filepath = NULL, name = NULL, chunkdim = NULL, level = NULL,
  type = c("double", "integer"), BPPARAM = bpparam())

## S4 method for signature 'HDF5Matrix'
rowsum(x, group, reorder = TRUE, na.rm = FALSE,
  filepath = NULL, name = NULL, chunkdim = NULL, level = NULL,
  type = c("double", "integer"), BPPARAM = bpparam())

Arguments

`x`	An HDF5Array::HDF5Matrix object.
`group`	A vector or factor giving the grouping, with one element per row of `x` for `rowsum()` or one element per column of `x` for `colsum()`. Missing values will be treated as another group and a warning will be given.
`reorder`	If `TRUE`, then the result will be in order of `sort(unique(group))`. If `FALSE`, it will be in the order that groups are encountered.
`na.rm`	logical (`TRUE` or `FALSE`). Should `NA` (including `NaN`) values be discarded?
`filepath`	`NULL` or the path (as a single string) to the (new or existing) HDF5 file where to write the dataset. If `NULL`, then the dataset will be written to the current HDF5 dump file i.e. the path returned by `HDF5Array::getHDF5DumpFile()` will be used.
`name`	`NULL` or the name of the HDF5 dataset to write. If `NULL`, then the name returned by `[HDF5Array::getHDF5DumpName()]` will be used.
`chunkdim`	The dimensions of the chunks to use for writing the data to disk. By default, `HDF5Array::getHDF5DumpChunkDim(dim(ans))` will be used, where `ans` is the returned object. See `?HDF5Array::getHDF5DumpChunkDim()` for more information.
`level`	The compression level to use for writing the data to disk. By default, `HDF5Array::getHDF5DumpCompressionLevel()` will be used. See `?HDF5Array::getHDF5DumpCompressionLevel()` for more information.
`type`	The type of the data that will be written to the HDF5Array object to create the result. If the result is known a priori to be `integer`, then it is recommended to set `type = "integer"`.
`BPPARAM`	An optional BiocParallel instance determining the parallel back-end to be used during evaluation, or a list of BiocParallel instances, to be applied in sequence for nested calls to BiocParallel functions.

Details

NOTE: Unlike base::rowsum(), the result is a base::double unless type = "integer" is specified. Notably, compared to base::rowsum(), this means that there are not the same issues with over/underflow in forming the sum results for integer arguments.

Examples

# A DelayedMatrix with a 'HDF5ArraySeed' seed
# NOTE: Requires that the HDF5Array package is installed
library(HDF5Array)
dm_HDF5 <- writeHDF5Array(matrix(c(rep(1L, 5),
                                   as.integer((0:4) ^ 2),
                                   seq(-5L, -1L, 1L)),
                                 ncol = 3))
group <- c(1, 1, 2)

# Compute the sums and store them in an HDF5-backed DelayedMatrix.
xsum <- colsum(dm_HDF5, group)
class(seed(xsum))

[Package DelayedMatrixStats version 1.4.0 Index]