Rlabkey (version 3.2.1)

labkey.experiment.createRun: 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)

Value

Returns the object representation of the experiment run object.

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

Author

Karl Lum

Details

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

See Also

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

Examples

if (FALSE) {

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
)

}