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Rlabkey (version 3.4.2)

Data Exchange Between R and 'LabKey' Server

Description

The 'LabKey' client library for R makes it easy for R users to load live data from a 'LabKey' Server, , into the R environment for analysis, provided users have permissions to read the data. It also enables R users to insert, update, and delete records stored on a 'LabKey' Server, provided they have appropriate permissions to do so.

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Version

Install

install.packages('Rlabkey')

Monthly Downloads

2,233

Version

3.4.2

License

Apache License 2.0

Maintainer

Cory Nathe

Last Published

March 13th, 2025

Functions in Rlabkey (3.4.2)

labkey.domain.createConditionalFormat

Create a conditional format data frame
labkey.domain.drop

Delete a LabKey domain
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.experiment.createData

Create an experiment data object
labkey.experiment.createMaterial

Create an experiment material object
labkey.experiment.lineage

Get lineage parent/child relationships for experiment objects
labkey.experiment.saveRuns

Saves Runs.
labkey.experiment.createRun

Create an experiment run object
labkey.experiment.saveBatch

Saves a modified experiment batch
labkey.executeSql

Retrieve data from a LabKey Server using SQL commands
labkey.experiment.SAMPLE_DERIVATION_PROTOCOL

Constant for the Simple Derivation Protocol
labkey.domain.get

Returns the metadata for an existing LabKey domain
labkey.getFolders

Retrieve a list of folders accessible to the current user
labkey.getLookupDetails

Retrieve detailed information on a LabKey query
labkey.importRows

Import rows of data into a LabKey Server
labkey.insertRows

Insert new rows of data into a LabKey Server
labkey.getBaseUrl

Get the default baseUrl parameter used for all http or https requests
labkey.makeRemotePath

Build a file path to data on a remote machine
labkey.getQueryDetails

Retrieve detailed information on a LabKey query
labkey.getModuleProperty

Get effective module property value
labkey.getQueryViews

Retrieve a list of available named views defined on a query in a schema
labkey.getQueries

Retrieve a list of available queries for a specified LabKey schema
labkey.moveRows

Move rows of data from a LabKey database
labkey.pipeline.startAnalysis

Start an analysis of a set of files using a pipeline
labkey.pipeline.getProtocols

Gets the protocols that have been saved for a particular pipeline
labkey.rstudio.saveReport

Update RStudio report source back to LabKey
labkey.rstudio.isInitialized

Check valid rlabkey session
labkey.getDefaultViewDetails

Retrieve the fields of a LabKey query view
labkey.provenance.stopRecording

Stop a provenance recording
labkey.provenance.startRecording

Start a provenance recording
labkey.rstudio.initReport

Initialize a RStudio session for LabKey R report source editing
labkey.getRequestOptions

Helper function to get the HTTP request options for a specific method type.
labkey.setDebugMode

Helper function to enable/disable debug mode.
labkey.setDefaults

Set the default parameters used for all http or https requests
labkey.rstudio.initSession

Initialize a RStudio session for LabKey integration using a time one request id
labkey.security.renameContainer

Rename an existing container at the given container path
labkey.saveBatch

Save an assay batch object to a labkey database
labkey.transform.readRunPropertiesFile

Assay transform script helper function to read a run properties file
labkey.security.stopImpersonating

Stop impersonating a user
labkey.getSchemas

Retrieve a list of available schemas from a labkey database
labkey.transform.getRunPropertyValue

Assay transform script helper function to get a run property value from a data.frame
labkey.security.moveContainer

Moves an existing container, which may be a folder or workbook
labkey.setModuleProperty

Set module property value
labkey.security.createContainer

Creates a new container, which may be a project, folder, or workbook, on the server
labkey.provenance.addRecordingStep

Add a step to a provenance recording
labkey.storage.update

Update a LabKey Freezer Manager storage item
labkey.security.deleteContainer

Deletes an existing container, which may be a project, folder, or workbook
labkey.security.impersonateUser

Start impersonating a user
labkey.provenance.createProvenanceParams

Create provenance parameter object
labkey.setWafEncoding

Helper function to enable/disable wafEncoding mode.
labkey.webdav.put

Upload a file via WebDAV
labkey.security.getContainers

Returns information about the specified container
lsFolders

List the available folder paths
labkey.rstudio.initRStudio

Initialize a RStudio session for LabKey integration
labkey.pipeline.getFileStatus

Gets the protocol file status for a pipeline
labkey.pipeline.getPipelineContainer

Gets the container in which the pipeline is defined
lsProjects

List the projects available at a given LabKey Server address
labkey.storage.create

Create a new LabKey Freezer Manager storage item
labkey.query.import

Bulk import an R data frame into a LabKey Server table using file import.
labkey.truncateTable

Delete all rows from a table
labkey.whoAmI

Call the whoami API
labkey.selectRows

Retrieve data from a labkey database
labkey.updateRows

Update existing rows of data in a labkey database
lsSchemas

List the available schemas
labkey.webdav.delete

Deletes the provided file/folder on a LabKey Server via WebDAV
labkey.setCurlOptions

Modify the current set of Curl options that are being used in the existing session
saveResults

Returns an object representing a LabKey schema
labkey.webdav.pathExists

Tests if a path exists on a LabKey Server via WebDAV
makeFilter

Builds filters to be used in labkey.selectRows and getRows
labkey.storage.delete

Delete a LabKey Freezer Manager storage item
labkey.webdav.listDir

List the contents of a LabKey Server folder via WebDAV
labkey.webdav.mkDirs

Create a folder via WebDAV
labkey.webdav.downloadFolder

Recursively download a folder via WebDAV
labkey.webdav.get

Download a file via WebDAV
labkey.webdav.mkDir

Create a folder via WebDAV
getLookups

Get related data fields that are available to include in a query on a given query object
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
Rlabkey-package

Exchange data between LabKey Server and R
labkey.domain.createConditionalFormatQueryFilter

Create a conditional format query filter
getFolderPath

Returns the folder path associated with a session
labkey.deleteRows

Delete rows of data from a LabKey database
getSchema

Returns an object representing a LabKey schema
getSession

Creates and returns a LabKey Server session
labkey.domain.FILTER_TYPES

Provide comparator access
getRows

Retrieve data from LabKey Server
labkey.domain.save

Updates an existing LabKey domain
labkey.domain.createAndLoad

Create a new LabKey domain and load data
labkey.domain.create

Create a new LabKey domain
labkey.domain.inferFields

Infer field metadata from a data frame