## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(
  echo = TRUE,
  warning = FALSE,
  message = FALSE,
  error = FALSE,
  eval = FALSE,
  tidy = FALSE,
  dev = c("png"),
  cache = TRUE
)

## ----example------------------------------------------------------------------
#  library(zellkonverter)
#  library(SingleCellExperiment)
#  
#  # Create SingleCellExperiment object that points to on-disk H5AD file
#  sce <- readH5AD(h5ad_file, use_hdf5 = TRUE)

## ----example2-----------------------------------------------------------------
#  # Read a series of H5AD files into a list
#  # then combine them into a single merged SingleCellExperiment
#  sce.lst <- lapply(h5ad_files, function(file) {
#    readH5AD(file, use_hdf5 = TRUE)
#  })
#  sce <- do.call(cbind, sce.list)

## ----example3-----------------------------------------------------------------
#  # read raw/ from H5AD file
#  # raw = TRUE tells readH5AD() to read alternative data
#  # Must use zellkonverter >=1.3.3
#  sce_in <- readH5AD(h5ad_file, use_hdf5 = TRUE, raw = TRUE)
#  
#  # use `raw` as counts
#  sce <- swapAltExp(sce_in, "raw") # use raw as main
#  counts(sce) <- assay(sce, "X") # set counts assay to data in X
#  assay(sce, "X") <- NULL # free X

## ----Seurat-------------------------------------------------------------------
#  library(SingleCellExperiment)
#  library(SeuratDisk)
#  
#  # Convert h5ad file to h5seurat format
#  Convert(h5ad_file, dest = "h5seurat")
#  
#  # load Seurat file
#  obj <- LoadH5Seurat(h5seurat_file)
#  
#  # Convert Seurat object to SingleCellExperiment
#  sce <- as.SingleCellExperiment(obj)

## ----session, echo=FALSE------------------------------------------------------
#  sessionInfo()