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
get_single_cell_experiment(
data,
assays = "counts",
cache_directory = get_default_cache_dir(),
repository = COUNTS_URL,
features = NULL
)A data frame containing, at minimum, a sample_ column, which
corresponds to a single cell sample ID. This can be obtained from the
get_metadata() function.
A character vector whose elements must be either "counts" and/or "cpm", representing the corresponding assay(s) you want to request. By default only the count assay is downloaded. If you are interested in comparing a limited amount of genes, the "cpm" assay is more appropriate.
An optional character vector of length one. If provided, it should indicate a local file path where any remotely accessed files should be copied.
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.
An optional character vector of features (ie genes) to return the counts for. By default counts for all features will be returned.
A SingleCellExperiment object, with one assay for each value in the assays argument
meta <- get_metadata() |> head(2)
sce <- get_single_cell_experiment(meta)
#> ℹ Realising metadata.
#> ℹ Synchronising files
#> ℹ Downloading 0 files, totalling 0 GB
#> ℹ Reading files.
#> ℹ Compiling Single Cell Experiment.