Create a custom dataset on the ScPCA Portal — create

Creates a new user dataset without starting processing. The returned list includes the dataset $id along with its current contents and status.

Usage

create_dataset(
  samples = NULL,
  projects = NULL,
  format = "sce",
  include_bulk = FALSE,
  email = NULL,
  auth_token = Sys.getenv("SCPCA_AUTH_TOKEN")
)

Arguments

samples: optional character vector of ScPCA sample IDs (e.g. "SCPCS000001")
projects: optional character vector of ScPCA project IDs (e.g. "SCPCP000001"); all samples from each project are included
format: the desired file format: "sce" (SingleCellExperiment, default) or "anndata" (AnnData/H5AD). Spatial data is not a valid format option here; spatial samples are always returned in Space Ranger format.
include_bulk: logical; whether to include bulk RNA-seq files. Default is FALSE.
email: optional email address for download notification
auth_token: an authorization token from get_auth(). Defaults to the SCPCA_AUTH_TOKEN environment variable, which get_auth() sets automatically.

Value

the API response as a list (invisibly), including the dataset $id

Examples

if (FALSE) { # \dontrun{
token <- get_auth("user@example.com", agree = TRUE)
ds <- create_dataset(
  auth_token = token,
  samples = c("SCPCS000001", "SCPCS000002")
)
ds$id
} # }