DataSpaceConnection | R Documentation |
The DataSpaceConnection class
The DataSpaceConnection class
connectDS
config
A list. Stores configuration of the connection object such as URL, path and username.
availableStudies
A data.table. The table of available studies.
availableGroups
A data.table. The table of available groups.
availablePublications
A data.table. The table of available publications.
mabGridSummary
A data.table. The filtered grid with updated
n_
columns and geometric_mean_curve_ic50
.
mabGrid
A data.table. The filtered mAb grid.
virusMetadata
A data.table. Metadata about all viruses in the DataSpace.
virusNameMappingTables
A list of data.table objects. This list contains 'virusMetadataAll', 'virusLabId', and 'virus_synonym' which are described in the vignette 'Virus_Name_Mapping_Tables'.
new()
Initialize a DataSpaceConnection
object.
See connectDS
.
DataSpaceConnection$new( login = NULL, password = NULL, verbose = FALSE, onStaging = FALSE )
login
A character. Optional argument. If there is no netrc file a temporary one can be written by passing login and password of an active DataSpace account.
password
A character. Optional. The password for the selected login.
verbose
A logical. Whether to print the extra details for troubleshooting.
onStaging
A logical. Whether to connect to the staging server instead of the production server.
A new 'DataSpaceConnection' object.
print()
Print the DataSpaceConnection
object.
DataSpaceConnection$print()
getStudy()
Create a DataSpaceStudy
object.
DataSpaceConnection$getStudy(studyName)
studyName
A character. Name of the study to retrieve.
getGroup()
Create a DataSpaceStudy
object.
DataSpaceConnection$getGroup(groupId)
groupId
An integer. ID of the group to retrieve.
filterMabGrid()
Filter rows in the mAb grid by specifying the values to keep in the
columns found in the mabGrid
field. It takes the column and the
values and filters the underlying tables.
DataSpaceConnection$filterMabGrid(using, value)
using
A character. Name of the column to filter.
value
A character vector. Values to keep in the mAb grid.
resetMabGrid()
Reset the mAb grid to the unfiltered state.
DataSpaceConnection$resetMabGrid()
getMab()
Create a DataSpaceMab
object.
DataSpaceConnection$getMab()
downloadPublicationData()
Download publication data for a chosen publication.
DataSpaceConnection$downloadPublicationData( publicationId, outputDir = getwd(), unzip = TRUE, verbose = TRUE )
publicationId
A character/integer. ID for the publication to download data for.
outputDir
A character. Path to directory to download publication data.
unzip
A logical. If TRUE, unzip publication data to outputDir.
verbose
A logical. Default TRUE.
refresh()
Refresh the connection object to update available studies and groups.
DataSpaceConnection$refresh()
clone()
The objects of this class are cloneable with this method.
DataSpaceConnection$clone(deep = FALSE)
deep
Whether to make a deep clone.
connectDS
DataSpaceR-package
## Not run: # Create a connection (Initiate a DataSpaceConnection object) con <- connectDS() con # Connect to cvd408 # https://dataspace.cavd.org/cds/CAVD/app.view#learn/learn/Study/cvd408?q=408 cvd408 <- con$getStudy("cvd408") # Connect to all studies cvd <- con$getStudy("cvd408") # Connect to the NYVAC durability comparison group # https://dataspace.cavd.org/cds/CAVD/app.view#group/groupsummary/220 nyvac <- con$getGroup(220) # Refresh the connection object to update available studies and groups con$refresh() ## End(Not run)
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