list_experiments | R Documentation |
Experiments can be represented by two object classes: Experiment
and
ExperimentIdentifier
. The fields that make up an ExperimentIdentifier
object are a subset of those required for an Experiment
object. Therefore
an experiment can be turned into an experiment id object without an API
call, using the function as_experiment_id()
. The reverse can be achieved
by calling list_experiments()
on experiment id objects. In general,
experiments and experiment id objects can be listed using
list_experiments()
and list_experiment_ids()
.
list_experiments(token, x, ...) ## S3 method for class 'ExperimentIdentifier' list_experiments(token, x, ...) ## S3 method for class 'Project' list_experiments(token, x, types = list_experiment_types(token), require = c(NA, "DataSets", "Samples"), ...) list_experiment_ids(token, ...) list_experiment_types(token, ...) as_experiment_id(x, ...) ## S3 method for class 'Experiment' as_experiment_id(x, ...) ## S3 method for class 'ExperimentIdentifier' as_experiment_id(x, ...)
token |
Login token as created by |
x |
Object to limit the number of returned experiments, e.g. a set of
|
... |
Generic compatibility. Extra arguments will be passed to
|
types |
Either a single or set of |
require |
A switch to require the resulting experiments to contain a nonzero number of dataset or sample. Default behavior is no requirement. |
By calling list_experiments()
on project objects, all corresponding
experiments are listed. It is possible to limit the search to experiments
that are of a certain type and exclude experiments that either have no
datasets or samples associated. An exhaustive list of realized experiment
types can be retrieved using list_experiment_types()
. If several
experiment types are requested in list_experiments()
, the default is to
iterate over all available types, an API call per experiment type has to be
made.
ExperimentIdentifier
objects present a more compact way of uniquely
representing experiments. All experiments that are available to the current
user can be listed with list_experiment_ids()
. There is no way of limiting
the search for experiments.
Depending on the number of resulting objects, either a
json_class
(single object) or a json_vec
(multiple objects), is
returned. Experiments are represented by Experiment
, experiment ids by
ExperimentIdentifier
and experiment types by ExperimentType
objects.
Other object listing functions: list_datasets
,
list_material
, list_plates
,
list_projects
, list_samples
tok <- login_openbis() # list all available projects to limit the search for experiments proj <- list_projects(tok) # list all experiments corresponding to the project with index 1 exps <- list_experiments(tok, proj[[1L]]) # convert experiment to experiment ids and back exp_ids <- as_experiment_id(exps) identical(exps, list_experiments(tok, exp_ids)) # experiments can also be searched for exp <- search_openbis(tok, search_criteria( attribute_clause("code", get_field(exps[[1L]], "identifier")) ), target_object = "experiment") identical(exps[[1L]], exp) logout_openbis(tok)
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