DelayedSubset-class: DelayedSubset objects

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

DelayedSubset objects

Description

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

The DelayedSubset class provides a formal representation of a delayed multi-dimensional single bracket subsetting operation. It is a concrete subclass of the DelayedUnaryOp virtual class, which itself is a subclass of the DelayedOp virtual class:

                          DelayedOp
                              ^
                              |
                        DelayedUnaryOp
                              ^
                              |
                        DelayedSubset
  

DelayedSubset objects are used inside a DelayedArray object to represent the delayed multi-dimensional single bracket subsetting 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 'DelayedSubset'
is_noop(x)

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

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

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

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

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

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

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

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

Arguments

x, object	A DelayedSubset 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

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

## ---------------------------------------------------------------------
## BASIC EXAMPLE
## ---------------------------------------------------------------------
a0 <- array(1:60, dim=5:3)
A0 <- DelayedArray(a0)
showtree(A0)

A <- A0[2:1, -4, 3, drop=FALSE]
showtree(A)
class(A@seed)        # a DelayedSubset object

## ---------------------------------------------------------------------
## PROPAGATION OF SPARSITY
## ---------------------------------------------------------------------
sm0 <- sparseMatrix(i=c(1, 4), j=c(1, 3), x=c(11, 43), dims=4:3)
SM0 <- DelayedArray(sm0)
showtree(SM0)
is_sparse(SM0)       # TRUE

SM1 <- SM0[-1, 3:2, drop=FALSE]
showtree(SM1)
class(SM1@seed)      # a DelayedSubset object
is_sparse(SM1@seed)  # TRUE

## Duplicated indices break structural sparsity.
M2 <- SM0[-1, c(3:2, 2), drop=FALSE]
showtree(M2)
class(M2@seed)       # a DelayedSubset object
is_sparse(M2@seed)   # FALSE

## ---------------------------------------------------------------------
## SANITY CHECKS
## ---------------------------------------------------------------------
stopifnot(class(A@seed) == "DelayedSubset")
stopifnot(class(SM1@seed) == "DelayedSubset")
stopifnot(is_sparse(SM1@seed))
stopifnot(class(M2@seed) == "DelayedSubset")
stopifnot(!is_sparse(M2@seed))

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