list_samples: List samples and sample types

In ropensci/infx: OpenBIS API Access to the InfectX Data Repository

List samples and sample types

Description

In openBIS, samples can be seen as a generalization of plates and wells ( see list_plates() and list_wells()). In fact, for the HTS focused openBIS instance of InfectX, wells and plates represent the only types of samples available. Samples can either be retrieved using search_openbis() and setting the argument target_object to sample or listed by calling list_samples(). Furthermore, all available sample types can be listed using list_sample_types().

Usage

list_samples(token, x, ...)

## S3 method for class 'ExperimentIdentifier'
list_samples(token, x, ...)

## S3 method for class 'Experiment'
list_samples(token, x, ...)

## S3 method for class 'Plate'
list_samples(token, x, ...)

## S3 method for class 'PlateIdentifier'
list_samples(token, x, ...)

## S3 method for class 'PlateMetadata'
list_samples(token, x, ...)

## S3 method for class 'WellIdentifier'
list_samples(token, x, ...)

## S3 method for class 'WellMetadata'
list_samples(token, x, ...)

list_sample_types(token, ...)

Arguments

token	Login token as created by login_openbis().
x	Object to limit the number of returned samples, e.g. a set of ExperimentIdentifier or Experiment objects.
...	Generic compatibility. Extra arguments will be passed to make_requests().

Details

list_samples() can be dispatched on objects identifying experiments (Experiment and ExperimentIdentifier), in which case the associated plate samples are returned, on objects representing plates (Plate, PlateIdentifier and PlateMetadata) or on objects representing wells (WellIdentifier and WellMetadata). For plates, the corresponding plate samples and for wells, the corresponding well samples are returned. It is therefore not possible to list all well samples for a plate. This could however be achieved by listing all wells of a plate using list_wells() and calling list_samples() on the returned set of WellIdentifier objects. A separate API call is required for each json_class object contained in the json_vec passed to list_samples() as x argument.

Value

Depending on the number of resulting objects, either a json_class (single object) or a json_vec (multiple objects), is returned. Sample objects as returned by list_samples() additionally inherit from the Sample class and sample type objects returned by list_sample_types() inherit from SampleType.

openBIS

• \Sexpr[results=rd]{infx::docs_link("gis", "listSamplesForExperiment")}
• \Sexpr[results=rd]{infx::docs_link("sas", "getPlateSample")}
• \Sexpr[results=rd]{infx::docs_link("sas", "getWellSample")}
• \Sexpr[results=rd]{infx::docs_link("gis", "listSampleTypes")}

See Also

Other object listing functions: list_datasets, list_experiments, list_material, list_plates, list_projects

Examples

  tok <- login_openbis()

  # search for an experiment, e.g. ADENO-AU-K1
  exp <- search_openbis(tok,
                        search_criteria(
                          property_clause("pathogen", "Adenovirus"),
                          property_clause("library", "Ambion"),
                          property_clause("geneset", "Kinome"),
                          property_clause("replicate", 1L)
                        ),
                        target_object = "experiment")

  # list all plate samples associated with this experiment
  plate_samp <- list_samples(tok, exp)
  length(plate_samp)

  # the same plates are returned using list_plates(), not regarding order
  plates <- list_plates(tok, exp)
  plate_samp <- plate_samp[order(get_field(plate_samp, "code"))]

  identical(as_plate_id(plates), as_plate_id(plate_samp))

  # plates can be converted to samples and back to plates again
  identical(as_plate_id(plates), as_plate_id(list_samples(tok, plates)))

  # the same is not possible for wells: first well ids are listed for a
  # plate
  well_ids <- list_wells(tok, plates[[1L]])
  # for efficiency only the first 5 wells are retained
  well_ids <- well_ids[1:5]
  print(well_ids, length = 10L)
  # the corresponding well samples are fetched
  well_samp <- list_samples(tok, well_ids)
  # from well sample objects it is not possible to directly create well id
  # objects as no plate id information is available
  print(well_samp, length = 20L)
  # with a bit of manual work however it is possible to create well id
  # objects from well samples
  wells <- well_id(get_field(well_samp, "permId"), plates[[1L]],
                   well_code = get_field(well_samp, "code"))
  identical(wells, well_ids)

  logout_openbis(tok)

ropensci/infx documentation built on May 14, 2022, 5:51 p.m.