DelayedAperm-class: DelayedAperm objects

In Bioconductor/DelayedArray: A unified framework for working transparently with on-disk and in-memory array-like datasets

DelayedAperm objects

Description

NOTE: This man page is about DelayedArray internals and is provided for developers and advanced users only.

The DelayedAperm class provides a formal representation of a delayed "extended aperm()" operation, that is, of a delayed aperm() that can drop and/or add ineffective dimensions. Note that since only ineffective dimensions (i.e. dimensions with an extent of 1) can be dropped or added, the length of the output array is guaranteed to be the same as the length of the input array.

DelayedAperm is a concrete subclass of the DelayedUnaryOp virtual class, which itself is a subclass of the DelayedOp virtual class:

                          DelayedOp
                              ^
                              |
                        DelayedUnaryOp
                              ^
                              |
                         DelayedAperm
  

DelayedAperm objects are used inside a DelayedArray object to represent the delayed "extended aperm()" operations carried by the object. They're never exposed to the end user and are not intended to be manipulated directly.

Usage

## S4 method for signature 'DelayedAperm'
is_noop(x)

## S4 method for signature 'DelayedAperm'
summary(object, ...)

## ~ ~ ~ Seed contract ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~

## S4 method for signature 'DelayedAperm'
dim(x)

## S4 method for signature 'DelayedAperm'
dimnames(x)

## S4 method for signature 'DelayedAperm'
extract_array(x, index)

## ~ ~ ~ Propagation of sparsity ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~

## S4 method for signature 'DelayedAperm'
is_sparse(x)

## S4 method for signature 'DelayedAperm'
extract_sparse_array(x, index)

Arguments

x, object	A DelayedAperm object.
index	See ?extract_array in the S4Arrays package for a description of the index argument.
...	Not used.

See Also

• DelayedOp objects.

• showtree to visualize the nodes and access the leaves in the tree of delayed operations carried by a DelayedArray object.

• extract_array in the S4Arrays package.

• extract_sparse_array in the SparseArray package.

Examples

## DelayedAperm extends DelayedUnaryOp which extends DelayedOp:
extends("DelayedAperm")

## ---------------------------------------------------------------------
## BASIC EXAMPLES
## ---------------------------------------------------------------------
a0 <- array(1:20, dim=c(1, 10, 2))
A0 <- DelayedArray(a0)
showtree(A0)

A <- aperm(A0, perm=c(2, 3, 1))
showtree(A)
class(A@seed)       # a DelayedAperm object

M1 <- drop(A0)
showtree(M1)
class(M1@seed)      # a DelayedAperm object

M2 <- t(M1)
showtree(M2)
class(M2@seed)      # a DelayedAperm object

## ---------------------------------------------------------------------
## PROPAGATION OF SPARSITY
## ---------------------------------------------------------------------
## DelayedAperm objects always propagate sparsity.

sa0 <- SparseArray(a0)
SA0 <- DelayedArray(sa0)
showtree(SA0)
is_sparse(SA0)      # TRUE

SA <- aperm(SA0, perm=c(2, 3, 1))
showtree(SA)
class(SA@seed)      # a DelayedAperm object
is_sparse(SA@seed)  # TRUE

## ---------------------------------------------------------------------
## SANITY CHECKS
## ---------------------------------------------------------------------
stopifnot(class(A@seed) == "DelayedAperm")
stopifnot(class(M1@seed) == "DelayedAperm")
stopifnot(class(M2@seed) == "DelayedAperm")
stopifnot(class(SA@seed) == "DelayedAperm")
stopifnot(is_sparse(SA@seed))

Bioconductor/DelayedArray documentation built on Aug. 8, 2024, 5:01 a.m.