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Add or remove samples and projects in a custom dataset

Source: R/datasets.R
modify_dataset_samples.Rd

add_dataset_samples() adds the given samples and/or all samples from the given projects to an existing dataset, keeping the samples already present. remove_dataset_samples() removes the given samples and/or projects, keeping the remaining samples; any project left with no samples is dropped from the dataset.

Usage

add_dataset_samples(
  dataset,
  samples = NULL,
  projects = NULL,
  include_bulk = FALSE,
  auth_token = Sys.getenv("SCPCA_AUTH_TOKEN")
)

remove_dataset_samples(
  dataset,
  samples = NULL,
  projects = NULL,
  auth_token = Sys.getenv("SCPCA_AUTH_TOKEN")
)

Arguments

dataset

the dataset UUID string, or a list with an $id element.

samples

optional character vector of ScPCA sample IDs to add or remove.

projects

optional character vector of ScPCA project IDs to add or remove; all samples from each project are included.

include_bulk

logical; for add_dataset_samples(), the includes_bulk value to use for projects that are newly added to the dataset. Existing projects keep their current value. Default is FALSE.

auth_token

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

Value

the updated dataset detail as a list (invisibly)

Details

In both cases the current dataset is fetched, its data is modified locally (taking the union per project and modality when adding, or dropping the specified IDs when removing), and the updated selection is sent back via a PUT request. To replace the dataset contents wholesale instead, use replace_dataset_data().

A dataset that has already been started cannot be modified. Projects whose single-cell data is merged (SINGLE_CELL = "MERGED") cannot be modified by sample (though they may be removed wholesale via projects); use replace_dataset_data() instead.

Examples

if (FALSE) { # \dontrun{
add_dataset_samples(ds, samples = "SCPCS000003")
add_dataset_samples(ds, projects = "SCPCP000002")

remove_dataset_samples(ds, samples = "SCPCS000003")
remove_dataset_samples(ds, projects = "SCPCP000002")
} # }