realizeFileBackedMatrix: Realize a file-backed DelayedMatrix

In LTLA/beachmat: Compiling Bioconductor to Handle Each Matrix Type

Realize a file-backed DelayedMatrix

Description

Realize a file-backed DelayedMatrix into its corresponding in-memory format.

Usage

realizeFileBackedMatrix(x)

isFileBackedMatrix(x)

Arguments

x	A DelayedMatrix object.

Details

A file-backed matrix representation is recognized based on whether it has a path method for any one of its seeds. If so, and the "beachmat.realizeFileBackedMatrix" option is not FALSE, we will load it into memory. This is intended for DelayedMatrix objects that have already been subsetted (e.g., to highly variable genes), which can be feasibly loaded into memory for rapid calculations.

Value

For realizeFileBackedMatrix, an ordinary matrix or a dgCMatrix, depending on whether is_sparse(x).

For isFileBackedMatrix, a logical scalar indicating whether x has file-backed components.

Author(s)

Aaron Lun

Examples

mat <- matrix(rnorm(50), ncol=5)
realizeFileBackedMatrix(mat) # no effect

library(HDF5Array)
mat2 <- as(mat, "HDF5Array")
realizeFileBackedMatrix(mat2) # realized into memory

LTLA/beachmat documentation built on Nov. 15, 2024, 10:19 p.m.