Create an in-memory AnnData object.

For more information on the functionality of an AnnData object, see AnnData-usage

Usage

AnnData(
  X = NULL,
  obs = NULL,
  var = NULL,
  layers = NULL,
  obsm = NULL,
  varm = NULL,
  obsp = NULL,
  varp = NULL,
  uns = NULL,
  shape = NULL
)

Arguments

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.

Value

An InMemoryAnnData object

See also

AnnData-usage for details of AnnData structure and usage

Other AnnData creators: as_AnnData(), read_h5ad()

Examples

adata <- AnnData(
  X = matrix(1:12, nrow = 3, ncol = 4),
  obs = data.frame(
    row.names = paste0("obs", 1:3),
    n_counts = c(1, 2, 3),
    n_cells = c(1, 2, 3)
  ),
  var = data.frame(
    row.names = paste0("var", 1:4),
    n_cells = c(1, 2, 3, 4)
  )
)

adata
#> InMemoryAnnData object with n_obs × n_vars = 3 × 4
#>     obs: 'n_counts', 'n_cells'
#>     var: 'n_cells'