Data Exchange Between R and 'LabKey' Server
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Documentation for package ‘Rlabkey’ version 2.10.0
Help Pages
| Rlabkey-package | Exchange data between LabKey Server and R |
| getFolderPath | Returns the folder path associated with a session |
| getLookups | Get related data fields that are available to include in a query on a given query object |
| getRows | Retrieve data from LabKey Server |
| getSchema | Returns an object representing a LabKey schema |
| getSession | Creates and returns a LabKey Server session |
| labkey.acceptSelfSignedCerts | Convenience method to configure Rlabkey connections to accept self-signed certificates |
| labkey.curlOptions | Returns the current set of Curl options that are being used in the existing session |
| labkey.deleteRows | Delete rows of data from a LabKey database |
| labkey.domain.create | Create a new LabKey domain |
| labkey.domain.createAndLoad | Create a new LabKey domain and load data |
| labkey.domain.createConditionalFormat | Create a conditional format data frame |
| labkey.domain.createConditionalFormatQueryFilter | Create a conditional format query filter |
| labkey.domain.createDesign | Helper function to create a domain design data structure |
| labkey.domain.createIndices | Helper function to create a domain design indices list |
| labkey.domain.drop | Delete a LabKey domain |
| labkey.domain.FILTER_TYPES | Provide comparator access |
| labkey.domain.get | Returns the metadata for an existing LabKey domain |
| labkey.domain.inferFields | Infer field metadata from a data frame |
| labkey.domain.save | Updates an existing LabKey domain |
| labkey.executeSql | Retrieve data from a LabKey Server using SQL commands |
| labkey.experiment.createData | Create an experiment data object |
| labkey.experiment.createMaterial | Create an experiment material object |
| labkey.experiment.createRun | Create an experiment run object |
| labkey.experiment.SAMPLE_DERIVATION_PROTOCOL | Constant for the Simple Derivation Protocol |
| labkey.experiment.saveBatch | Saves a modified experiment batch |
| labkey.experiment.saveRuns | Saves Runs. |
| labkey.getBaseUrl | Get the default baseUrl parameter used for all http or https requests |
| labkey.getDefaultViewDetails | Retrieve the fields of a LabKey query view |
| labkey.getFolders | Retrieve a list of folders accessible to the current user |
| labkey.getLookupDetails | Retrieve detailed information on a LabKey query |
| labkey.getModuleProperty | Get effective module property value |
| labkey.getQueries | Retrieve a list of available queries for a specified LabKey schema |
| labkey.getQueryDetails | Retrieve detailed information on a LabKey query |
| labkey.getQueryViews | Retrieve a list of available named views defined on a query in a schema |
| labkey.getRequestOptions | Helper function to get the HTTP request options for a specific method type. |
| labkey.getSchemas | Retrieve a list of available schemas from a labkey database |
| labkey.importRows | Import rows of data into a LabKey Server |
| labkey.insertRows | Insert new rows of data into a LabKey Server |
| labkey.makeRemotePath | Build a file path to data on a remote machine |
| labkey.pipeline.getFileStatus | Gets the protocol file status for a pipeline |
| labkey.pipeline.getPipelineContainer | Gets the container in which the pipeline is defined |
| labkey.pipeline.getProtocols | Gets the protocols that have been saved for a particular pipeline |
| labkey.pipeline.startAnalysis | Start an analysis of a set of files using a pipeline |
| labkey.provenance.addRecordingStep | Add a step to a provenance recording |
| labkey.provenance.createProvenanceParams | Create provenance parameter object |
| labkey.provenance.startRecording | Start a provenance recording |
| labkey.provenance.stopRecording | Stop a provenance recording |
| labkey.query.import | Bulk import an R data frame into a LabKey Server table using file import. |
| labkey.rstudio.initReport | Initialize a RStudio session for LabKey R report source editing |
| labkey.rstudio.initRStudio | Initialize a RStudio session for LabKey integration |
| labkey.rstudio.initSession | Initialize a RStudio session for LabKey integration using a time one request id |
| labkey.rstudio.isInitialized | Check valid rlabkey session |
| labkey.rstudio.saveReport | Update RStudio report source back to LabKey |
| labkey.saveBatch | Save an assay batch object to a labkey database |
| labkey.security.createContainer | Creates a new container, which may be a project, folder, or workbook, on the server |
| labkey.security.deleteContainer | Deletes an existing container, which may be a project, folder, or workbook |
| labkey.security.getContainers | Returns information about the specified container |
| labkey.security.impersonateUser | Start impersonating a user |
| labkey.security.moveContainer | Moves an existing container, which may be a folder or workbook |
| labkey.security.stopImpersonating | Stop impersonating a user |
| labkey.selectRows | Retrieve data from a labkey database |
| labkey.setCurlOptions | Modify the current set of Curl options that are being used in the existing session |
| labkey.setDebugMode | Helper function to enable/disable debug mode. |
| labkey.setDefaults | Set the default parameters used for all http or https requests |
| labkey.setModuleProperty | Set module property value |
| labkey.storage.create | Create a new LabKey Freezer Manager storage item |
| labkey.storage.delete | Delete a LabKey Freezer Manager storage item |
| labkey.storage.update | Update a LabKey Freezer Manager storage item |
| labkey.transform.getRunPropertyValue | Assay transform script helper function to get a run property value from a data.frame |
| labkey.transform.readRunPropertiesFile | Assay transform script helper function to read a run properties file |
| labkey.truncateTable | Delete all rows from a table |
| labkey.updateRows | Update existing rows of data in a labkey database |
| labkey.webdav.delete | Deletes the provided file/folder on a LabKey Server via WebDAV |
| labkey.webdav.downloadFolder | Recursively download a folder via WebDAV |
| labkey.webdav.get | Download a file via WebDAV |
| labkey.webdav.listDir | List the contents of a LabKey Server folder via WebDAV |
| labkey.webdav.mkDir | Create a folder via WebDAV |
| labkey.webdav.mkDirs | Create a folder via WebDAV |
| labkey.webdav.pathExists | Tests if a path exists on a LabKey Server via WebDAV |
| labkey.webdav.put | Upload a file via WebDAV |
| labkey.whoAmI | Call the whoami API |
| lsFolders | List the available folder paths |
| lsProjects | List the projects available at a given LabKey Server address |
| lsSchemas | List the available schemas |
| makeFilter | Builds filters to be used in labkey.selectRows and getRows |
| Rlabkey | Exchange data between LabKey Server and R |
| saveResults | Returns an object representing a LabKey schema |