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Get a summary of a custom ScPCA dataset

Source: R/datasets.R
get_dataset_info.Rd

Fetches a custom dataset and returns a structured summary of its contents, including its processing status and a per-sample table describing the modality of each sample.

Usage

get_dataset_info(dataset, auth_token = Sys.getenv("SCPCA_AUTH_TOKEN"))

Arguments

dataset

the dataset UUID string (such as the value returned by create_dataset()), or a list with an $id element (such as the value returned by this function).

auth_token

an authorization token from get_auth(). Defaults to the SCPCA_AUTH_TOKEN environment variable, which get_auth() sets automatically.

Value

a named list with the following elements:

  • id: the dataset UUID string

  • format: the dataset file format (e.g. "SINGLE_CELL_EXPERIMENT", "ANN_DATA")

  • status: the processing status — one of "pending", "processing", "succeeded", "failed", or "expired" (see get_dataset_status())

  • n_samples: the total number of samples in the dataset, taken from the API's total_sample_count

  • n_projects: the number of projects in the dataset

  • sample_info: a data frame with one row per included sample and the following columns:

    • scpca_sample_id

    • scpca_project_id

    • seq_unit ("cell" or "nucleus", or NA if the sample is not included as single-cell)

    • has_spatial

    • has_bulk

    • has_cite_seq

    • has_multiplexed

  • merged_projects: a character vector of project IDs whose single-cell data is merged; character(0) when none

Details

For each project, the included samples and their modality details are looked up from the project's sample records (one request per project), so merged projects (whose individual sample IDs are not enumerated in the dataset record) are expanded to all of their single-cell samples. Projects whose single-cell data is merged are also listed in merged_projects.

Examples

if (FALSE) { # \dontrun{
ds_id <- create_dataset(samples = c("SCPCS000001", "SCPCS000002"))
info <- get_dataset_info(ds_id)
info$status
info$sample_info
} # }