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
)Arguments
- data
A data frame containing, at minimum,
cell_id,file_id_cellNexus_pseudobulk,sample_id,cell_type_unified_ensemble,atlas_idcolumns, 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/06-02-2025) for internal use. They can be obtained from theget_metadata()function.- assays
A character vector specifying the desired assay(s) to be requested. Valid elements include "counts", "cpm", and "rank" for single-cell analyses, or "counts" for pseudobulk analyses. The default setting retrieves only the counts assay. If your analysis involves a smaller set of genes, consider using the "cpm" assay. The "rank" assay is suited for signature calculations across millions of cells.
- 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.
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)
#> ℹ Downloading 1 file, totalling 0 GB
#> ℹ Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellNexus-metadata/sample_metadata.1.3.0.parquet to /github/home/.cache/R/cellNexus/sample_metadata.1.3.0.parquet
pseudobulk <- meta |> get_pseudobulk()
#> ℹ Realising metadata.
#> ℹ Synchronising files
#> ℹ Reading files.
#> ℹ Compiling Experiment.