DataSpaceStudy | R Documentation |
The DataSpaceStudy class
The DataSpaceStudy class
DataSpaceConnection$getStudy()
DataSpaceConnection$getGroup()
study
A character. The study name.
config
A list. Stores configuration of the connection object such as URL, path and username.
availableDatasets
A data.table. The table of datasets available in
the DataSpaceStudy
object.
cache
A list. Stores the data to avoid downloading the same tables multiple times.
dataDir
A character. Default directory for storing nonstandard
datasets. Set with setDataDir(dataDir)
.
treatmentArm
A data.table. The table of treatment arm information for the connected study. Not available for all study connection.
group
A character. The group name.
studyInfo
A list. Stores the information about the study.
new()
Initialize DataSpaceStudy
class.
See DataSpaceConnection
.
DataSpaceStudy$new(study = NULL, config = NULL, group = NULL, studyInfo = NULL)
study
A character. Name of the study to retrieve.
config
A list. Stores configuration of the connection object such as URL, path and username.
group
An integer. ID of the group to retrieve.
studyInfo
A list. Stores the information about the study.
print()
Print DataSpaceStudy
class.
DataSpaceStudy$print()
getDataset()
Get a dataset from the connection.
DataSpaceStudy$getDataset( datasetName, mergeExtra = FALSE, colFilter = NULL, reload = FALSE, outputDir = NULL, ... )
datasetName
A character. Name of the dataset to retrieve.
Accepts the value in either the "name" or "label" field from availableDatasets
.
mergeExtra
A logical. If set to TRUE, merge extra information. Ignored for non-integrated datasets.
colFilter
A matrix. A filter as returned by Rlabkey's
makeFilter
.
reload
A logical. If set to TRUE, download the dataset, whether a cached version exist or not.
outputDir
A character. Optional, specifies directory to download
nonstandard datasets. If NULL
, data will be downloaded to
dataDir
, set with setDataDir(dataDir)
. If dataDir
is not set, and outputDir
is NULL
, a tmp directory will be
used.
...
Extra arguments to be passed to
labkey.selectRows
clearCache()
Clear cache
. Remove downloaded datasets.
DataSpaceStudy$clearCache()
getDatasetDescription()
Get variable information.
DataSpaceStudy$getDatasetDescription(datasetName, outputDir = NULL)
datasetName
A character. Name of the dataset to retrieve.
Accepts the value in either the "name" or "label" field from availableDatasets
.
outputDir
A character. Directory path.
setDataDir()
Set default directory to download non-integrated datasets. If no
dataDir
is set, a tmp directory will be used.
DataSpaceStudy$setDataDir(dataDir)
dataDir
A character. Directory path.
refresh()
Refresh the study object to update available datasets and treatment info.
DataSpaceStudy$refresh()
clone()
The objects of this class are cloneable with this method.
DataSpaceStudy$clone(deep = FALSE)
deep
Whether to make a deep clone.
connectDS
DataSpaceConnection
## Not run: # Create a connection (Initiate a DataSpaceConnection object) con <- connectDS() # Connect to cvd408 (Initiate a DataSpaceStudy object) # https://dataspace.cavd.org/cds/CAVD/app.view#learn/learn/Study/cvd408?q=408 cvd408 <- con$getStudy("cvd408") cvd408 # Retrieve Neutralizing antibody dataset (NAb) for cvd408 from DataSpace NAb <- cvd408$getDataset("NAb") # Get variable information of the NAb dataset cvd408$getDatasetDescription("NAb") # Take a look at cvd408's treatment arm information cvd408$treatmentArm # Clear cache of a study object cvd408$clearCache() # Connect to the NYVAC durability comparison group # https://dataspace.cavd.org/cds/CAVD/app.view#group/groupsummary/220 nyvac <- con$getGroup(220) # Connect to all studies cvd <- con$getStudy("") # Refresh the study object to update available datasets and treatment info cvd$refresh() ## End(Not run)
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