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Rlabkey (version 3.2.0)

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

902

Version

3.2.0

License

Apache License 2.0

Maintainer

Cory Nathe

Last Published

January 9th, 2024

Functions in Rlabkey (3.2.0)

labkey.domain.save

Updates an existing LabKey domain

labkey.experiment.createData

Create an experiment data object

labkey.experiment.saveRuns

labkey.experiment.saveBatch

Saves a modified experiment batch

labkey.experiment.createRun

Create an experiment run object

labkey.experiment.createMaterial

Create an experiment material object

labkey.executeSql

Retrieve data from a LabKey Server using SQL commands

labkey.domain.inferFields

Infer field metadata from a data frame

labkey.domain.get

Returns the metadata for an existing LabKey domain

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.experiment.SAMPLE_DERIVATION_PROTOCOL

Constant for the Simple Derivation Protocol

labkey.importRows

Import rows of data into a LabKey Server

labkey.getLookupDetails

Retrieve detailed information on a LabKey query

labkey.getSchemas

Retrieve a list of available schemas from a labkey database

labkey.getModuleProperty

Get effective module property value

labkey.getQueryViews

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

labkey.getQueryDetails

Retrieve detailed information on a LabKey query

labkey.makeRemotePath

Build a file path to data on a remote machine

labkey.getRequestOptions

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

labkey.insertRows

Insert new rows of data into a LabKey Server

labkey.getQueries

Retrieve a list of available queries for a specified LabKey schema

labkey.provenance.createProvenanceParams

Create provenance parameter object

labkey.provenance.startRecording

Start a provenance recording

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.moveRows

Move rows of data from a LabKey database

labkey.query.import

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

labkey.provenance.addRecordingStep

Add a step to a provenance recording

labkey.rstudio.initSession

Initialize a RStudio session for LabKey integration using a time one request id

labkey.pipeline.getFileStatus

Gets the protocol file status for a pipeline

labkey.provenance.stopRecording

Stop a provenance recording

labkey.pipeline.startAnalysis

Start an analysis of a set of files using a pipeline

labkey.rstudio.isInitialized

Check valid rlabkey session

labkey.rstudio.saveReport

Update RStudio report source back to LabKey

labkey.rstudio.initRStudio

Initialize a RStudio session for LabKey integration

labkey.rstudio.initReport

Initialize a RStudio session for LabKey R report source editing

labkey.security.impersonateUser

Start impersonating a user

labkey.security.deleteContainer

Deletes an existing container, which may be a project, folder, or workbook

labkey.saveBatch

Save an assay batch object to a labkey database

labkey.security.getContainers

Returns information about the specified container

labkey.security.createContainer

Creates a new container, which may be a project, folder, or workbook, on the server

labkey.setModuleProperty

Set module property value

labkey.setCurlOptions

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

labkey.setDefaults

Set the default parameters used for all http or https requests

labkey.security.stopImpersonating

Stop impersonating a user

labkey.setDebugMode

Helper function to enable/disable debug mode.

labkey.security.renameContainer

Rename an existing container at the given container path

labkey.setWafEncoding

Helper function to enable/disable wafEncoding mode.

labkey.security.moveContainer

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

labkey.storage.create

Create a new LabKey Freezer Manager storage item

labkey.selectRows

Retrieve data from a labkey database

labkey.truncateTable

Delete all rows from a table

labkey.storage.delete

Delete a LabKey Freezer Manager storage item

labkey.storage.update

Update a LabKey Freezer Manager storage item

labkey.webdav.get

Download a file via WebDAV

labkey.webdav.listDir

List the contents of a LabKey Server folder via WebDAV

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.webdav.delete

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

labkey.webdav.downloadFolder

Recursively download a folder via WebDAV

labkey.updateRows

Update existing rows of data in a labkey database

List the available folder paths

List the available schemas

List the projects available at a given LabKey Server address

Call the whoami API

Builds filters to be used in labkey.selectRows and getRows

labkey.webdav.pathExists

Tests if a path exists on a LabKey Server via WebDAV

labkey.webdav.put

Upload a file via WebDAV

Returns an object representing a LabKey schema

labkey.webdav.mkDirs

Create a folder via WebDAV

labkey.webdav.mkDir

Create a folder via WebDAV

Returns an object representing a LabKey schema

labkey.domain.FILTER_TYPES

Provide comparator access

Creates and returns a LabKey Server session

labkey.domain.createConditionalFormat

Create a conditional format data frame

labkey.deleteRows

Delete rows of data from a LabKey database

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

labkey.domain.createDesign

Helper function to create a domain design data structure

labkey.domain.createConditionalFormatQueryFilter

Create a conditional format query filter

Retrieve data from LabKey Server

labkey.domain.createIndices

Helper function to create a domain design indices list

Rlabkey-package

Exchange data between LabKey Server and R

Returns the folder path associated with a session

labkey.domain.drop

Delete a LabKey domain

labkey.curlOptions

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

labkey.acceptSelfSignedCerts

Convenience method to configure Rlabkey connections to accept self-signed certificates

labkey.domain.createAndLoad

Create a new LabKey domain and load data

labkey.domain.create

Create a new LabKey domain