## ----include=TRUE,results="hide",message=FALSE,warning=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) # show method smallMatrix dim(smallMatrix) ## ----------------------------------------------------------------------------- testh5 <- tempfile(fileext = ".h5") writeHDF5Array(smallMatrix, filepath = testh5, name = "smallMatrix", with.dimnames = TRUE) ## ----------------------------------------------------------------------------- h5ls(testh5) ## ----------------------------------------------------------------------------- hdf5Data <- HDF5ArraySeed(file = testh5, name = "smallMatrix") newDelayedMatrix <- DelayedArray(hdf5Data) class(newDelayedMatrix) newDelayedMatrix ## ----------------------------------------------------------------------------- HDF5MAE <- MultiAssayExperiment(experiments = list(smallMatrix = smallMatrix)) sampleMap(HDF5MAE) colData(HDF5MAE) ## ----------------------------------------------------------------------------- HDF5SE <- SummarizedExperiment(assays = smallMatrix) assay(HDF5SE) MultiAssayExperiment(list(HDF5SE = HDF5SE))