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Rlabkey (version 2.9.0)

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

877

Version

2.9.0

License

Apache License 2.0

Maintainer

Cory Nathe

Last Published

September 21st, 2022

Functions in Rlabkey (2.9.0)

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.acceptSelfSignedCerts

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

Creates and returns a LabKey Server session

labkey.domain.get

Returns the metadata for an existing LabKey domain

labkey.domain.FILTER_TYPES

Provide comparator access

labkey.domain.createAndLoad

Create a new LabKey domain and load data

labkey.domain.createIndices

Helper function to create a domain design indices list

labkey.domain.createConditionalFormat

Create a conditional format data frame

labkey.domain.createDesign

Helper function to create a domain design data structure

labkey.getBaseUrl

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

labkey.domain.save

Updates an existing LabKey domain

labkey.experiment.saveBatch

Saves a modified experiment batch

labkey.domain.createConditionalFormatQueryFilter

Create a conditional format query filter

labkey.domain.inferFields

Infer field metadata from a data frame

labkey.experiment.SAMPLE_DERIVATION_PROTOCOL

Constant for the Simple Derivation Protocol

labkey.domain.create

Create a new LabKey domain

labkey.domain.drop

Delete a LabKey domain

labkey.executeSql

Retrieve data from a LabKey Server using SQL commands

labkey.getDefaultViewDetails

Retrieve the fields of a LabKey query view

labkey.getRequestOptions

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

labkey.getLookupDetails

Retrieve detailed information on a LabKey query

labkey.getSchemas

Retrieve a list of available schemas from a labkey database

labkey.getFolders

Retrieve a list of folders accessible to the current user

labkey.experiment.saveRuns

labkey.experiment.createData

Create an experiment data object

labkey.getQueryDetails

Retrieve detailed information on a LabKey query

labkey.getModuleProperty

Get effective module property value

labkey.experiment.createMaterial

Create an experiment material object

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.experiment.createRun

Create an experiment run object

labkey.importRows

Import rows of data into a LabKey Server

labkey.insertRows

Insert new rows of data into a LabKey Server

labkey.pipeline.getPipelineContainer

Gets the container in which the pipeline is defined

labkey.query.import

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

labkey.makeRemotePath

Build a file path to data on a remote machine

labkey.pipeline.getProtocols

Gets the protocols that have been saved for a particular pipeline

labkey.provenance.stopRecording

Stop a provenance recording

labkey.pipeline.getFileStatus

Gets the protocol file status for a pipeline

labkey.provenance.addRecordingStep

Add a step to a provenance recording

labkey.pipeline.startAnalysis

Start an analysis of a set of files using a pipeline

labkey.rstudio.saveReport

Update RStudio report source back to LabKey

labkey.rstudio.initSession

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

labkey.provenance.createProvenanceParams

Create provenance parameter object

labkey.provenance.startRecording

Start a provenance recording

labkey.security.deleteContainer

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

labkey.rstudio.isInitialized

Check valid rlabkey session

labkey.security.createContainer

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

labkey.saveBatch

Save an assay batch object to a labkey database

labkey.security.getContainers

Returns information about the specified container

labkey.security.impersonateUser

Start impersonating a user

labkey.setCurlOptions

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

labkey.security.stopImpersonating

Stop impersonating a user

labkey.rstudio.initReport

Initialize a RStudio session for LabKey R report source editing

labkey.rstudio.initRStudio

Initialize a RStudio session for LabKey integration

labkey.storage.delete

Delete a LabKey Freezer Manager storage item

labkey.storage.update

Update a LabKey Freezer Manager storage item

labkey.setModuleProperty

Set module property value

labkey.setDefaults

Set the default parameters used for all http or https requests

labkey.security.moveContainer

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

labkey.selectRows

Retrieve data from a labkey database

labkey.storage.create

Create a new LabKey Freezer Manager storage item

labkey.setDebugMode

Helper function to enable/disable debug mode.

labkey.transform.getRunPropertyValue

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

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

List the available folder paths

labkey.webdav.pathExists

Tests if a path exists on a LabKey Server via WebDAV

labkey.webdav.put

Upload a file via WebDAV

Call the whoami API

labkey.webdav.listDir

List the contents of a LabKey Server folder via WebDAV

labkey.updateRows

Update existing rows of data in a labkey database

labkey.truncateTable

Delete all rows from a table

Returns an object representing a LabKey schema

Builds filters to be used in labkey.selectRows and getRows

labkey.webdav.mkDirs

Create a folder via WebDAV

labkey.webdav.mkDir

Create a folder via WebDAV

labkey.transform.readRunPropertiesFile

Assay transform script helper function to read a run properties file

List the projects available at a given LabKey Server address

List the available schemas

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

Returns an object representing a LabKey schema

Returns the folder path associated with a session

Rlabkey-package

Exchange data between LabKey Server and R

RlabkeyUsersGuide

Open the Rlabkey Users Guide

Retrieve data from LabKey Server