getObservations: Obtain the observation values for the clinical data of a...

In thehyve/heim-RInterface: R Client for accessing the tranSMART RESTful API

Description

This function will retrieve the observation values for the clinical data of a certain study. A subset of observations can be selected by filtering by concept.

Usage

getObservations(study.name, concept.match = NULL, concept.links = NULL, as.data.frame = TRUE)

Arguments

study.name	a character string giving the name of a study.
concept.match	a character string or character vector containing the concept name(s) that should be matched. For each vector element, the getObservations function will search within the requested study for the first concept which name contains the given character string. It uses the name column of the result from getConcepts to perform the matching.
concept.links	a character string or a character vector containing the link(s) pointing to the locations of the chosen concepts on the server. Candidate values for this argument can be found in the api.link.self.href column of the getConcepts results. It is the most exact way to refer to a concept, and it overwrites the concept.match argument.
as.data.frame	logical (default setting is TRUE): should the list containing the observation values be converted to a dataframe?

Value

When as.data.frame is set to TRUE (default setting), a list is returned containing three data.frame objects:

observations	a dataframe containing the actual clinical observation values. Each row corresponds to one subject, whereby the first column contains the subject.id. Each other column contains values pertaining to a single concept.
subjectInfo	a dataframe containing additional information on each of the subjects.
conceptInfo	a dataframe that maps the column names of the 'observations' data.frame to their corresponding concept labels as they are defined within tranSMART.

If as.data.frame is set to FALSE, a list is contained with a structure very similar to how it is received from the server.

Note

To be able to access a transmart database, you need to be connected to the server the database is on. If you haven't connected to the server yet, establish a connection using the connectToTransmart function.

Author(s)

Tim Dorscheidt, Jan Kanis, Rianne Jansen. Contact: [e-mail]

See Also

getStudies, getConcepts

Examples

## Not run: 
  # The following will retrieve a list with observations for the study "foo"
  getObservations("foo")
  
## End(Not run)

thehyve/heim-RInterface documentation built on May 31, 2019, 9:12 a.m.