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_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. Valid elements include "counts", "cpm", "rank", and "sct" for single-cell 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.

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.