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

get_seurat(...)

Arguments

...

Arguments passed on to get_single_cell_experiment

data: 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.
assays: 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.
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.
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.
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()

Examples

meta <- get_metadata() |> head(2)
seurat <- get_seurat(meta)
#> ℹ Realising metadata.
#> ℹ Synchronising files
#> ℹ Downloading 0 files, totalling 0 GB
#> ℹ Reading files.
#> ℹ Compiling Single Cell Experiment.