Create an experiment run object
Create an experiment run object.
labkey.experiment.createRun(config,
dataInputs = NULL, dataOutputs = NULL, dataRows = NULL,
materialInputs = NULL, materialOutputs = NULL, plateMetadata = NULL)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 |
Create an experiment run object which can be used in the saveBatch function.
Returns the object representation of the experiment run object.
Karl Lum
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
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