## ---- echo=FALSE, warning=FALSE-------------------------------------------- suppressPackageStartupMessages({ library(MultiAssayExperiment) library(HDF5Array) library(SummarizedExperiment) }) ## ---- eval = FALSE--------------------------------------------------------- # library(MultiAssayExperiment) # library(HDF5Array) # library(SummarizedExperiment) ## -------------------------------------------------------------------------- smallMatrix <- matrix(rnorm(10e5), ncol = 20) ## -------------------------------------------------------------------------- rownames(smallMatrix) <- paste0("GENE", seq_len(nrow(smallMatrix))) colnames(smallMatrix) <- paste0("SampleID", seq_len(ncol(smallMatrix))) ## -------------------------------------------------------------------------- smallMatrix <- DelayedArray(smallMatrix) class(smallMatrix) head(smallMatrix) dim(smallMatrix) ## -------------------------------------------------------------------------- dataLocation <- system.file("extdata", "exMatrix.h5", package = "MultiAssayExperiment", mustWork = TRUE) h5ls(dataLocation) hdf5Data <- HDF5ArraySeed(file = dataLocation, name = "exMatrix") newDelayedMatrix <- DelayedArray(hdf5Data) class(newDelayedMatrix) head(newDelayedMatrix) ## -------------------------------------------------------------------------- HDF5MAE <- MultiAssayExperiment(experiments = list(smallMatrix = smallMatrix)) sampleMap(HDF5MAE) colData(HDF5MAE) ## -------------------------------------------------------------------------- HDF5SE <- SummarizedExperiment(assays = smallMatrix) assay(HDF5SE) MultiAssayExperiment(list(HDF5SE = HDF5SE))