In waldronlab/MultiAssayExperiment: Software for the integration of multi-omics experiments in Bioconductor

Integrating an HDF5 backend for MultiAssayExperiment

Dependencies

library(MultiAssayExperiment)
library(HDF5Array)
library(SummarizedExperiment)

HDF5Array and DelayedArray Constructor

The HDF5Array package provides an on-disk representation of large datasets without the need to load them into memory. Convenient lazy evaluation operations allow the user to manipulate such large data files based on metadata. The DelayedMatrix class in the DelayedArray package provides a way to connect to a large matrix that is stored on disk.

First, we create a small matrix for constructing the DelayedMatrix class.

smallMatrix <- matrix(rnorm(10e5), ncol = 20)

We add rownames and column names to the matrix object for compatibility with the MultiAssayExperiment representation.

rownames(smallMatrix) <- paste0("GENE", seq_len(nrow(smallMatrix)))
colnames(smallMatrix) <- paste0("SampleID", seq_len(ncol(smallMatrix)))

Here we use the DelayedArray constructor function to create a DelayedMatrix object.

smallMatrix <- DelayedArray(smallMatrix)
class(smallMatrix)
# show method
smallMatrix

dim(smallMatrix)

Writing to a file with dimnames

Finally, the rhdf5 package stores dimnames in a standard location.

In order to make use of this functionality, we would use writeHDF5Array with the with.dimnames argument:

testh5 <- tempfile(fileext = ".h5")
writeHDF5Array(smallMatrix, filepath = testh5, name = "smallMatrix",
    with.dimnames = TRUE)

To see the file structure we use h5ls:

h5ls(testh5)

Importing HDF5 files

Note that a large matrix from an HDF5 file can also be loaded using the HDF5ArraySeed and DelayedArray functions.

hdf5Data <- HDF5ArraySeed(file = testh5, name = "smallMatrix")
newDelayedMatrix <- DelayedArray(hdf5Data)
class(newDelayedMatrix)
newDelayedMatrix

Using a `DelayedMatrix` with `MultiAssayExperiment`

A DelayedMatrix alone conforms to the MultiAssayExperiment API requirements. Shown below, the DelayedMatrix can be put into a named list and passed into the MultiAssayExperiment constructor function.

HDF5MAE <- MultiAssayExperiment(experiments = list(smallMatrix = smallMatrix))
sampleMap(HDF5MAE)
colData(HDF5MAE)

`SummarizedExperiment` with `DelayedMatrix` backend

A more information rich DelayedMatrix can be created when used in conjunction with the SummarizedExperiment class and it can even include rowRanges. The flexibility of the MultiAssayExperiment API supports classes with minimal requirements. Additionally, this SummarizedExperiment with the DelayedMatrix backend can be part of a bigger MultiAssayExperiment object. Below is a minimal example of how this would work:

HDF5SE <- SummarizedExperiment(assays = smallMatrix)
assay(HDF5SE)
MultiAssayExperiment(list(HDF5SE = HDF5SE))

Additional scenarios are currently in development where an HDF5Matrix is hosted remotely. Many opportunities exist when considering on-disk and off-disk representations of data with MultiAssayExperiment.