Gets a Metacell from curated metadata — get

Given a data frame of Curated Atlas metadata obtained from get_metadata(), returns a SingleCellExperiment::SingleCellExperiment object corresponding to the samples in that data frame

Usage

get_metacell(
  data,
  assays = "counts",
  cell_aggregation,
  cache_directory = get_default_cache_dir(),
  repository = COUNTS_URL,
  features = NULL
)

Source

Mangiola et al.,2023

Arguments

data: A data frame containing, at minimum, sample_id, file_id_cellNexus_single_cell, atlas_id and a metacell column (e.g metacell_2) columns, which correspond to sample ID file subdivision for internal use, atlas name in format (e.g cellxgene/06-02-2025) for internal use, and metacell column to be queried. They can be obtained from the get_metadata() function.
assays: A character vector of metacell counts. Default to "counts".
cell_aggregation: A character vector representing the level of metacell aggregation. It indicates a group of cells that can be divided into the number of metacells. Each metacell comprises a minimum of ten single cells by default.
cache_directory: An optional character vector of length one. If provided, it should indicate a local file path where any remotely accessed files should be copied.
repository: A character vector of length one. If provided, it should be an HTTP URL pointing to the location where the single cell data is stored.
features: An optional character vector of features (ie genes) to return the counts for. By default counts for all features will be returned. When provided, the returned object will contain exactly the requested features (row order preserved), and any experiments/samples that do not contain all requested features are dropped. This preserves the full set of requested features at the cost of potentially fewer samples. A warning is emitted when samples are dropped.

Value

A SingleCellExperiment object.

References

Mangiola, S., M. Milton, N. Ranathunga, C. S. N. Li-Wai-Suen, A. Odainic, E. Yang, W. Hutchison et al. "A multi-organ map of the human immune system across age, sex and ethnicity." bioRxiv (2023): 2023-06. doi:10.1101/2023.06.08.542671.

Examples

# Use the lightweight sample database URL (for fast checks during development only)
meta <- get_metadata(cloud_metadata = cellNexus::SAMPLE_DATABASE_URL) |> head(2)
metacell <- meta |> get_metacell(cell_aggregation = "metacell_2")
#> ℹ Realising metadata.
#> ℹ Synchronising files
#> ℹ Reading files.
#> ℹ Compiling Experiment.