readH5AD {zellkonverter} | R Documentation

## Read H5AD

### Description

Reads a H5AD file and returns a SingleCellExperiment object.

### Usage

    readH5AD(
      file,
      X_name = NULL,
      use_hdf5 = FALSE,
      reader = c("python", "R"),
      verbose = NULL,
      ...
    )

### Arguments

`file` | String containing a path to a `.h5ad` file.
`X_name` | Name used when saving `X` as an assay. If `NULL` looks for an `X_name` value in `uns`, otherwise uses `"X"`.
`use_hdf5` | Logical scalar indicating whether assays should be loaded as HDF5-based matrices from the HDF5Array package.
`reader` | Which HDF5 reader to use. Either `"python"` for reading with the anndata Python package via reticulate or `"R"` for zellkonverter's native R reader.
`verbose` | Logical scalar indicating whether to print progress messages. If `NULL` uses `getOption("zellkonverter.verbose")`.
`...` | Arguments passed on to `AnnData2SCE` `layers` Arguments specifying how these slots are converted. If `TRUE` everything in that slot is converted, if `FALSE` nothing is converted and if a character vector only those items or columns are converted. `uns` Arguments specifying how these slots are converted. If `TRUE` everything in that slot is converted, if `FALSE` nothing is converted and if a character vector only those items or columns are converted. `var` Arguments specifying how these slots are converted. If `TRUE` everything in that slot is converted, if `FALSE` nothing is converted and if a character vector only those items or columns are converted. `obs` Arguments specifying how these slots are converted. If `TRUE` everything in that slot is converted, if `FALSE` nothing is converted and if a character vector only those items or columns are converted. `varm` Arguments specifying how these slots are converted. If `TRUE` everything in that slot is converted, if `FALSE` nothing is converted and if a character vector only those items or columns are converted. `obsm` Arguments specifying how these slots are converted. If `TRUE` everything in that slot is converted, if `FALSE` nothing is converted and if a character vector only those items or columns are converted. `varp` Arguments specifying how these slots are converted. If `TRUE` everything in that slot is converted, if `FALSE` nothing is converted and if a character vector only those items or columns are converted. `obsp` Arguments specifying how these slots are converted. If `TRUE` everything in that slot is converted, if `FALSE` nothing is converted and if a character vector only those items or columns are converted. `raw` Arguments specifying how these slots are converted. If `TRUE` everything in that slot is converted, if `FALSE` nothing is converted and if a character vector only those items or columns are converted. `skip_assays` Logical scalar indicating whether to skip conversion of any assays in `sce` or `adata`, replacing them with empty sparse matrices instead.

### Details

Setting `use_hdf5 = TRUE` allows for very large datasets to be efficiently represented on machines with little memory. However, this comes at the cost of access speed as data needs to be fetched from the HDF5 file upon request.

When first run, this function will instantiate a conda environment containing all of the necessary dependencies. This will not be performed on any subsequent run or if any other zellkonverter function has been run prior to this one.

Setting `reader = "R"` will use an experimental native R reader instead of reading the file into Python and converting the result. This avoids the need for a Python environment and some of the issues with conversion but is still under development and is likely to return slightly different output.

### Value

A SingleCellExperiment object is returned.

### Author(s)

Luke Zappia

Aaron Lun

### See Also

`writeH5AD()`, to write a SingleCellExperiment object to a H5AD file.

`AnnData2SCE()`, for developers to convert existing AnnData instances to a SingleCellExperiment.

### Examples

    library(SummarizedExperiment)

    file <- system.file("extdata", "krumsiek11.h5ad", package = "zellkonverter")
    sce <- readH5AD(file)
    class(assay(sce))

    sce2 <- readH5AD(file, use_hdf5 = TRUE)
    class(assay(sce2))

    sce3 <- readH5AD(file, reader = "R")

[Package zellkonverter version 1.4.0 Index]