Gets a Pseudobulk from curated metadata

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

Usage

get_pseudobulk(
  data,
  assays = "counts",
  cell_aggregation = "pseudobulk",
  cache_directory = get_default_cache_dir(),
  repository = COUNTS_URL,
  features = NULL,
  as_SummarizedExperiment = FALSE
)

Source

Mangiola et al.,2023

Arguments

data

A data frame containing, at minimum, cell_id, file_id_cellNexus_pseudobulk, sample_id, cell_type_unified_ensemble, atlas_id columns, which correspond to a single cell ID, file subdivision for internal use, a singlel cell sample ID, harmonised cell type, and atlas name in format (e.g cellxgene_2024/0.1.0) for internal use. They can be obtained from the get_metadata() function. Use get_atlas_versions() to download atlas versions data frame.

assays

A character vector specifying the desired assay(s) to be requested. The default setting retrieves only the counts assay.

cell_aggregation

A character vector that specifies which cell aggregation strategy should be applied. This will create a corresponding subdirectory in the cache directory.

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.

as_SummarizedExperiment

If TRUE, coerce the result to a SummarizedExperiment. Note that as(x, "SummarizedExperiment") drops feature rownames; get_pseudobulk() restores them after coercion.

Value

By default, a SingleCellExperiment object. If as_SummarizedExperiment is TRUE, a SummarizedExperiment 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) |>
  keep_quality_cells() |>
  dplyr::filter(cell_type_unified_ensemble == "epithelial")
pseudobulk <- meta |> get_pseudobulk()
#> ℹ Realising metadata.
#> ℹ Synchronising files
#> ℹ Reading files.
#> ℹ Compiling Experiment.