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Implementation of an HDF5-backed AnnData object.

See AnnData-usage for details on creating and using AnnData objects.

See also

AnnData-usage for details on creating and using AnnData objects

Other AnnData classes: AbstractAnnData, InMemoryAnnData

Super class

anndataR::AbstractAnnData -> HDF5AnnData

Active bindings

X

See AnnData-usage

layers

See AnnData-usage

obsm

See AnnData-usage

varm

See AnnData-usage

obsp

See AnnData-usage

varp

See AnnData-usage

obs

See AnnData-usage

var

See AnnData-usage

obs_names

See AnnData-usage

var_names

See AnnData-usage

uns

See AnnData-usage

Methods

Inherited methods


Method new()

Close the HDF5 file when the object is garbage collected

HDF5AnnData constructor

Usage

HDF5AnnData$new(
  file,
  X = NULL,
  obs = NULL,
  var = NULL,
  layers = NULL,
  obsm = NULL,
  varm = NULL,
  obsp = NULL,
  varp = NULL,
  uns = NULL,
  shape = NULL,
  mode = c("r", "r+", "a", "w", "w-", "x"),
  compression = c("none", "gzip", "lzf")
)

Arguments

file

The file name (character) of the .h5ad file. If this file already exits, other arguments must be NULL.

X

See the X slot in AnnData-usage

obs

See the obs slot in AnnData-usage

var

See the var slot in AnnData-usage

layers

See the layers slot in AnnData-usage

obsm

See the obsm slot in AnnData-usage

varm

See the varm slot in AnnData-usage

obsp

See the obsp slot in AnnData-usage

varp

See the varp slot in AnnData-usage

uns

See the uns slot in AnnData-usage

shape

Shape tuple (e.g. c(n_obs, n_vars)). Can be provided if both X or obs and var are not provided.

mode

The mode to open the HDF5 file. See as_HDF5AnnData() for details

compression

The compression algorithm to use. See as_HDF5AnnData() for details

Details

The constructor creates a new HDF5 AnnData interface object. This can either be used to either connect to an existing .h5ad file or to create a new one. To create a new file both obs_names and var_names must be specified. In both cases, any additional slots provided will be set on the created object. This will cause data to be overwritten if the file already exists.


Method close()

Close the HDF5 file

Usage

HDF5AnnData$close()


Method n_obs()

See the n_obs field in AnnData-usage

Usage

HDF5AnnData$n_obs()


Method n_vars()

See the n_vars field in AnnData-usage

Usage

HDF5AnnData$n_vars()