experiments: Experiment Endpoints

In CytobankAPI: Cytobank API Wrapper for R

Experiment Endpoints

Description

Interact with experiment endpoints. An Experiment is a container for data and analyses in Cytobank. If data are on Cytobank, they must be within an Experiment. Configurations such as gates, compensations, scales, Sample Tags, and illustrations are also linked to an individual Experiment. Within the Cytobank interface, the Experiment Summary Page is a useful integration point for information about an Experiment.

Usage

## S4 method for signature 'UserSession'
experiments.clone_full(
  UserSession,
  experiment_id,
  output = "default",
  timeout = UserSession@long_timeout
)

## S4 method for signature 'UserSession'
experiments.clone_selective(
  UserSession,
  experiment_id,
  experiment_name,
  fcs_files = c(-1),
  primary_researcher = NA,
  principal_investigator = NA,
  clone_gates = FALSE,
  clone_annotations = FALSE,
  clone_attachments = FALSE,
  clone_reagents = FALSE,
  clone_compensations = FALSE,
  clone_panels = FALSE,
  clone_illustrations = FALSE,
  clone_project = FALSE,
  clone_user_access = FALSE,
  allow_full_access_pi = FALSE,
  output = "default",
  timeout = UserSession@long_timeout
)

## S4 method for signature 'UserSession'
experiments.delete(
  UserSession,
  experiment_id,
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession'
experiments.full_access_users_list(
  UserSession,
  experiment_id,
  output = "default",
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession'
experiments.full_access_users_add(
  UserSession,
  experiment_id,
  user_id = NA,
  user_email = NA,
  username = NA,
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession'
experiments.full_access_users_remove(
  UserSession,
  experiment_id,
  user_id = NA,
  user_email = NA,
  username = NA,
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession'
experiments.list(
  UserSession,
  output = "default",
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession'
experiments.new(
  UserSession,
  experiment_name,
  purpose,
  comments = NA,
  primary_researcher = NA,
  principal_investigator = NA,
  output = "default",
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession'
experiments.show(
  UserSession,
  experiment_id,
  output = "default",
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession'
experiments.trash(
  UserSession,
  experiment_id,
  output = "default",
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession'
experiments.update(
  UserSession,
  experiment,
  output = "default",
  timeout = UserSession@short_timeout
)

Arguments

UserSession	Cytobank UserSession object
experiment_id	integer representing an experiment ID
output	character representing the output format [optional] - experiments.clone_full, experiments.clone_selective, experiments.full_access_users_list, experiments.list, experiments.new, experiments.show, experiments.trash, experiments.update : ("default", "raw")
timeout	integer representing the request timeout time in seconds [optional]
experiment_name	character representing an experiment name
fcs_files	vector/list of integers representing a list of FCS file IDs [optional]
primary_researcher	integer representing a primary researcher ID [optional]
principal_investigator	integer representing a principal investigator ID [optional]
clone_gates	boolean denoting cloning gates option [optional]
clone_annotations	boolean denoting cloning annotations option [optional]
clone_attachments	boolean denoting cloning attachments option [optional]
clone_reagents	boolean denoting cloning reagents option [optional]
clone_compensations	boolean denoting cloning compensations option [optional]
clone_panels	boolean denoting cloning panels option [optional]
clone_illustrations	boolean denoting cloning illustrations option [optional]
clone_project	boolean denoting cloning project option [optional]
clone_user_access	boolean denoting cloning user access option [optional]
allow_full_access_pi	boolean denoting to allow full access to PI option [optional]
user_id	integer representing a user's ID
user_email	character representing a user's email
username	character representing a username
purpose	character representing an experiment purpose
comments	character representing an experiment comment [optional]
experiment	dataframe representing an experiment

Details

experiments.clone_full Full clone an experiment. Learn more about the full clone functionality.
- Optional output parameter, specify one of the following: ("default", "raw")

experiments.clone_selective Selectively clone an experiment. Learn more about the selective clone functionality
- Optional output parameter, specify one of the following: ("default", "raw")

experiments.delete Permanently delete an experiment and all analyses (including SPADE, viSNE, etc.) permanently. This is not reversible.

experiments.list List all full access users from an experiment.
- Optional output parameter, specify one of the following: ("default", "raw")

experiments.list Add a full access user to an experiment. A full access user can be added by a user ID, email, or username.

experiments.list Remove a full access user from an experiment. A full access user can be removed by a user ID, email, or username.

experiments.list List all inbox experiments. Outputs a data frame [default] or raw list with all fields present.
- Optional output parameter, specify one of the following: ("default", "raw")

experiments.new Create a new experiment.
- Optional output parameter, specify one of the following: ("default", "raw")

experiments.show Show experiment details.
- Optional output parameter, specify one of the following: ("default", "raw")

experiments.trash Trash an experiment. This is reversible and not to be confused with permanent deletion.

experiments.update Update an experiment. (all parameters are optional, except for experiment_id)
- Optional output parameter, specify one of the following: ("default", "raw")

Examples

## Not run: # Authenticate via username/password
cyto_session <- authenticate(site="premium", username="cyril_cytometry", password="cytobank_rocks!")
# Authenticate via auth_token
cyto_session <- authenticate(site="premium", auth_token="my_secret_auth_token")

## End(Not run)
## Not run: experiments.clone_full(cyto_session, 22)

## Not run: experiments.clone_selective(cyto_session, 22,
  experiment_name="My New Experiment Name", fcs_files=c(12, 13, 14, 15, 16))

## End(Not run)
## Not run: experiments.delete(cyto_session, 22)

## Not run: # Dataframe of all full access users
experiments.full_access_users_list(cyto_session, 22)

# List of all full access users
experiments.full_access_users_list(cyto_session, 22, output="raw")

## End(Not run)
## Not run: # Add a user as a full access user by user's ID
experiments.full_access_users_add(cyto_session, 22, user_id=2)

# Add a user as a full access user by user's email
experiments.full_access_users_add(cyto_session, 22, user_email="[e-mail]")

# Add a user as a full access user by user's username
experiments.full_access_users_add(cyto_session, 22, username="sammy_cytometry")

## End(Not run)
## Not run: # Remove a user as a full access user by user's ID
experiments.full_access_users_remove(cyto_session, 22, user_id=2)

# Remove a user as a full access user by user's email
experiments.full_access_users_remove(cyto_session, 22, user_email="[e-mail]")

# Remove a user as a full access user by user's username
experiments.full_access_users_remove(cyto_session, 22, username="sammy_cytometry")

## End(Not run)
## Not run: # Dataframe of all inbox experiments with all fields present
experiments.list(cyto_session)

# Raw list of all inbox experiments with all fields present
experiments.list(cyto_session, output="raw")

## End(Not run)
## Not run: experiments.new(cyto_session, "My New Experiment Name", "My experiment purpose",
  "An optional comment")

## End(Not run)
## Not run: experiments.show(cyto_session, 22)

## Not run: experiments.trash(cyto_session, 22)

## Not run: experiments.update(cyto_session, experiment=cyto_experiment)

CytobankAPI documentation built on April 21, 2023, 9:08 a.m.