labkey.experiment.createRun: Create an experiment run object

In Rlabkey: Data Exchange Between R and 'LabKey' Server

Create an experiment run object

Description

Create an experiment run object.

Usage

labkey.experiment.createRun(config,
    dataInputs = NULL, dataOutputs = NULL, dataRows = NULL,
    materialInputs = NULL, materialOutputs = NULL, plateMetadata = NULL)

Arguments

config	a list of base experiment object properties
dataInputs	(optional) a list of experiment data objects to be used as data inputs to the run
dataOutputs	(optional) a list of experiment data objects to be used as data outputs to the run
dataRows	(optional) a data frame containing data rows to be uploaded to the assay backed run
materialInputs	(optional) a list of experiment material objects to be used as material inputs to the run
materialOutputs	(optional) a list of experiment material objects to be used as material outputs to the run
plateMetadata	(optional) if the assay supports plate templates, the plate metadata object to upload

Details

Create an experiment run object which can be used in the saveBatch function.

Value

Returns the object representation of the experiment run object.

Author(s)

Karl Lum

See Also

labkey.experiment.saveBatch, labkey.experiment.createData, labkey.experiment.createMaterial

Examples

## Not run: 

library(Rlabkey)

## create a non-assay backed run with samples as material inputs and outputs

m1 <- labkey.experiment.createMaterial(
        list(name = "87444063.2604.626"), sampleSetName = "Study Specimens")
m2 <- labkey.experiment.createMaterial(
        list(name = "87444063.2604.625"), sampleSetName = "Study Specimens")
run <- labkey.experiment.createRun(
        list(name="new run"), materialInputs = m1, materialOutputs = m2)
labkey.experiment.saveBatch(baseUrl="http://labkey/", folderPath="home",
        protocolName=labkey.experiment.SAMPLE_DERIVATION_PROTOCOL, runList=run)

## import an assay run which includes plate metadata

df <- data.frame(participantId=c(1:3), visitId = c(10,20,30), welllocation = c("A1", "D11", "F12"))

runConfig <- fromJSON(txt='{"assayId": 310,
    "name" : "api imported run with plate metadata",
    "properties" : {
        "PlateTemplate" : "urn:lsid:labkey.com:PlateTemplate.Folder-6:d8bbec7d-34cd-1038-bd67-b3bd"
    }
}')

plateMetadata <- fromJSON(txt='{
      "control" : {
        "positive" : {"dilution":  0.005},
        "negative" : {"dilution":  1.0}
      },
      "sample" : {
        "SA01" : {"dilution": 1.0, "ID" : 111, "Barcode" : "BC_111", "Concentration" : 0.0125},
        "SA02" : {"dilution": 2.0, "ID" : 222, "Barcode" : "BC_222"},
        "SA03" : {"dilution": 3.0, "ID" : 333, "Barcode" : "BC_333"},
        "SA04" : {"dilution": 4.0, "ID" : 444, "Barcode" : "BC_444"}
      }
    }')

run <- labkey.experiment.createRun(runConfig, dataRows = df, plateMetadata = plateMetadata)
labkey.experiment.saveBatch(
    baseUrl="http://labkey/", folderPath="home",
    assayConfig=list(assayId = 310), runList=run
)


## End(Not run)

Rlabkey documentation built on Nov. 8, 2023, 1:06 a.m.