Given a data frame of HCA metadata, returns a Seurat object corresponding to the samples in that data frame

Usage

get_seurat(...)

Source

Mangiola et al.,2023

Arguments

...

Arguments passed on to get_single_cell_experiment

data: A data frame containing, at minimum, cell_id, file_id_cellNexus_single_cell and atlas_id columns, which correspond to a single cell ID, file subdivision for internal use, and atlas name in format (e.g cellxgene/06-02-2025) for internal use. They can be obtained from the get_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. Single cell level is applied 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. 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. 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. 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 Seurat object containing the same data as a call to get_single_cell_experiment()

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)
seurat <- get_seurat(meta)
#> ℹ Realising metadata.
#> ℹ Synchronising files
#> ℹ Reading files.
#> ℹ Compiling Experiment.