DelayedAbind-class: DelayedAbind objects

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

DelayedAbind objects

Description

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

The DelayedAbind class provides a formal representation of a delayed abind() operation. It is a concrete subclass of the DelayedNaryOp virtual class, which itself is a subclass of the DelayedOp virtual class:

                          DelayedOp
                              ^
                              |
                        DelayedNaryOp
                              ^
                              |
                        DelayedAbind
  

DelayedAbind objects are used inside a DelayedArray object to represent the delayed abind() 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 'DelayedAbind'
is_noop(x)

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

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

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

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

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

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

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

## S4 method for signature 'DelayedAbind'
OLD_extract_sparse_array(x, index)

Arguments

x, object	A DelayedAbind 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.

• OLD_extract_sparse_array.

Examples

## DelayedAbind extends DelayedNaryOp which extends DelayedOp:
extends("DelayedAbind")

## ---------------------------------------------------------------------
## BASIC EXAMPLE
## ---------------------------------------------------------------------
m1 <- matrix(101:128, ncol=4)
m2 <- matrix(runif(16), ncol=4)
M1 <- DelayedArray(m1)
M2 <- DelayedArray(m2)
showtree(M1)
showtree(M2)

M3 <- rbind(M1, M2)
showtree(M3)
class(M3@seed)        # a DelayedAbind object

M4 <- cbind(t(M1), M2)
showtree(M4)
class(M4@seed)        # a DelayedAbind object

## ---------------------------------------------------------------------
## PROPAGATION OF SPARSITY
## ---------------------------------------------------------------------
## DelayedAbind objects always propagate sparsity (granted that all the
## input arrays are sparse).

sm1 <- sparseMatrix(i=c(1, 1, 7, 7), j=c(1, 4, 1, 4),
                    x=c(11, 14, 71, 74), dims=c(7, 4))
SM1 <- DelayedArray(sm1)
sm2 <- sparseMatrix(i=c(1, 1, 4, 4), j=c(1, 4, 1, 4),
                    x=c(11, 14, 41, 44), dims=c(4, 4))
SM2 <- DelayedArray(sm2)
showtree(SM1)
showtree(SM2)
is_sparse(SM1)        # TRUE
is_sparse(SM2)        # TRUE

SM3 <- rbind(SM1, SM2)
showtree(SM3)
class(SM3@seed)       # a DelayedAbind object
is_sparse(SM3@seed)   # TRUE

SM4 <- cbind(SM2, t(SM1))
showtree(SM4)
class(SM4@seed)       # a DelayedAbind object
is_sparse(SM4@seed)   # TRUE

M5 <- rbind(SM2, M1)  # 2nd input array is not sparse!
showtree(M5)
class(M5@seed)        # a DelayedAbind object
is_sparse(M5@seed)    # FALSE

## ---------------------------------------------------------------------
## SANITY CHECKS
## ---------------------------------------------------------------------
stopifnot(class(M3@seed) == "DelayedAbind")
stopifnot(class(M4@seed) == "DelayedAbind")
stopifnot(class(SM3@seed) == "DelayedAbind")
stopifnot(is_sparse(SM3@seed))
stopifnot(class(SM4@seed) == "DelayedAbind")
stopifnot(is_sparse(SM4@seed))
stopifnot(class(M5@seed) == "DelayedAbind")
stopifnot(!is_sparse(M5@seed))

Bioconductor/DelayedArray documentation built on March 4, 2024, 9:12 p.m.