Load a Muon-style h5ad file into a memory_daf.

Loads dense or sparse /X, /obs and /var column groups (dense scalar columns and categorical columns), flat + nested /uns scalar entries (nested keys are flattened via _), dense /layers, and /obsm / /varm dense matrices (each stored on a synthetic axis obsm_<name>_dim / varm_<name>_dim). obsp / varp and raw are still escalated through unsupported_handler and skipped.

Usage

h5ad_as_daf(path, name = NULL, mode = "r", unsupported_handler = WARN_HANDLER)

Arguments

path

Path to the .h5ad file.

name

Optional name for the returned Daf; defaults to the file basename without extension.

mode

hdf5r open mode. Default "r" (read-only).

unsupported_handler

Handler for h5ad features we don't translate (default WARN_HANDLER). Accepts ERROR_HANDLER, WARN_HANDLER, IGNORE_HANDLER, or a function(message) dispatched via inefficient_action_handler().

Value

A memory_daf() populated with the h5ad contents.

Details

Requires the hdf5r and Matrix packages.

See also

daf_as_h5ad(), DafAnnData, as_anndata()

Examples

if (FALSE) { # \dontrun{
p <- system.file("extdata", "small_test.h5ad", package = "dafr")
d <- h5ad_as_daf(p)
is_daf(d)
} # }