## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval = FALSE------------------------------------------------------------- # library(remotes) # remotes::install_github("ilia-kats/MuData") ## ----setup, message = FALSE--------------------------------------------------- library(MuData) library(MultiAssayExperiment) library(rhdf5) ## ----------------------------------------------------------------------------- data(miniACC) miniACC ## ----------------------------------------------------------------------------- writeH5MU(miniACC, "miniacc.h5mu") ## ----------------------------------------------------------------------------- rhdf5::h5ls("miniacc.h5mu", recursive = FALSE) ## ----------------------------------------------------------------------------- h5 <- rhdf5::H5Fopen("miniacc.h5mu") h5&'mod' rhdf5::H5close() ## ----------------------------------------------------------------------------- acc <- readH5MU("miniacc.h5mu") acc ## ----------------------------------------------------------------------------- head(colData(miniACC)[,1:4]) head(colData(acc)[,1:4]) ## ----------------------------------------------------------------------------- head(rowData(miniACC[["gistict"]])) head(rowData(acc[["gistict"]])) ## ----------------------------------------------------------------------------- acc_b <- readH5MU("miniacc.h5mu", backed = TRUE) assay(acc_b, "RNASeq2GeneNorm")[1:5,1:3] ## ----------------------------------------------------------------------------- class(assay(acc_b, "RNASeq2GeneNorm")) ## ----------------------------------------------------------------------------- assay(acc, "RNASeq2GeneNorm")[1:5,1:3] class(assay(acc, "RNASeq2GeneNorm")) ## ----------------------------------------------------------------------------- sessionInfo()