updated manual

transmart · Aug 22, 2016 · 95084d0 · 95084d0
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diff --git a/R/getObservations.R b/R/getObservations.R
@@ -22,8 +22,8 @@
 # You should have received a copy of the GNU General Public License along
 # with this program. If not, see <http://www.gnu.org/licenses/>.
 
-getObservations <- function(study.name, concept.match = NULL, concept.links = NULL, as.data.frame = TRUE, 
-                            patient.set = NULL) {
+getObservations <- function(study.name, concept.match = NULL, concept.links = NULL, patient.set = NULL, 
+                            as.data.frame = TRUE) {
     .ensureTransmartConnection()
 
     if (is.null(concept.links)) {

diff --git a/man/getHighdimData.Rd b/man/getHighdimData.Rd
@@ -48,7 +48,8 @@ The remaining parameters are constraints that limit the amount of data that is r
 Assay constraints:
 
   \item{trial.name}{A single character string with the trial name.}
-  \item{patient.set}{A number indicating the patient set.}
+  \item{patient.set}{A number indicating the patient set, as created with \code{\link{createPatientSet}}.
+  It can be used to retrieve only the data for the patients that belong to that specific patient.set}
   \item{ontology.term}{A single character string containing the concept path.}
   \item{assay.ids}{A numeric vector containing the id's of the assays you want to retrieve.}
   \item{patient.ids}{A character vector with the patient ids that you want to retrieve.}

diff --git a/man/getObservations.Rd b/man/getObservations.Rd
@@ -8,12 +8,14 @@
   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)
+getObservations(study.name, concept.match = NULL, concept.links = NULL, patient.set = NULL, as.data.frame = TRUE)
 }
 \arguments{
   \item{study.name}{a character string giving the name of a study.}
   \item{concept.match}{a character string or character vector containing the concept name(s) that should be matched. For each vector element, the \code{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 \code{\link{getConcepts}} to perform the matching.}
   \item{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 \code{api.link.self.href} column of the \code{\link{getConcepts}} results. It is the most exact way to refer to a concept, and it overwrites the \code{concept.match} argument.}
+  \item{patient.set}{ A number indicating the patient set, as created with \code{\link{createPatientSet}}.
+  It can be used to retrieve only the data for the patients that belong to that specific patient.set}
   \item{as.data.frame}{logical (default setting is TRUE): should the list containing the observation values be converted to a dataframe?}
 }
 \details{