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
anndataR::AbstractAnnData$as_HDF5AnnData()
anndataR::AbstractAnnData$as_InMemoryAnnData()
anndataR::AbstractAnnData$as_Seurat()
anndataR::AbstractAnnData$as_SingleCellExperiment()
anndataR::AbstractAnnData$layers_keys()
anndataR::AbstractAnnData$obs_keys()
anndataR::AbstractAnnData$obsm_keys()
anndataR::AbstractAnnData$obsp_keys()
anndataR::AbstractAnnData$print()
anndataR::AbstractAnnData$shape()
anndataR::AbstractAnnData$to_HDF5AnnData()
anndataR::AbstractAnnData$to_InMemoryAnnData()
anndataR::AbstractAnnData$to_Seurat()
anndataR::AbstractAnnData$to_SingleCellExperiment()
anndataR::AbstractAnnData$uns_keys()
anndataR::AbstractAnnData$var_keys()
anndataR::AbstractAnnData$varm_keys()
anndataR::AbstractAnnData$varp_keys()
anndataR::AbstractAnnData$write_h5ad()
Method new()
Close the HDF5 file when the object is garbage collected
HDF5AnnData
constructor
Usage
HDF5AnnData$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 beNULL
.X
See the
X
slot in AnnData-usageobs
See the
obs
slot in AnnData-usagevar
See the
var
slot in AnnData-usagelayers
See the
layers
slot in AnnData-usageobsm
See the
obsm
slot in AnnData-usagevarm
See the
varm
slot in AnnData-usageobsp
See the
obsp
slot in AnnData-usagevarp
See the
varp
slot in AnnData-usageuns
See the
uns
slot in AnnData-usageshape
Shape tuple (e.g.
c(n_obs, n_vars)
). Can be provided if bothX
orobs
andvar
are not provided.mode
The mode to open the HDF5 file. See
as_HDF5AnnData()
for detailscompression
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.