Rlabkey (version 2.1.121)

labkey.saveBatch: Save an assay batch object to a labkey database

Description

Save an assay batch object to a labkey database

Usage

labkey.saveBatch(baseUrl, folderPath, assayName, resultDataFrame, batchPropertyList=NULL, runPropertyList=NULL)

Arguments

baseUrl

a string specifying the baseUrlfor the labkey server

folderPath

a string specifying the folderPath

assayName

a string specifying the name of the assay instance

resultDataFrame

a data frame containing rows of data to be inserted

batchPropertyList

a list of batch Properties

runPropertyList

a list of run Properties

Value

• Returns the object representation of the Assay batch.

Details

To save an R data.frame an assay results sets, you must create a named assay using the "General" assay provider. Detailed instructions are avaialable in the Rlabkey Users Guide, accessible by entering RlabkeyUsersGuide() at the R command prompt. Note that saveBatch currently supports only a single run with one result set per batch.

References

https://www.labkey.org/wiki/home/Documentation/page.view?name=createDatasetViaAssay

See Also

labkey.selectRows, labkey.executeSql, makeFilter, labkey.updateRows, labkey.deleteRows

Examples

## Very simple example of an analysis flow:  query some data, calculate some stats,
## then save the calculations as an assay result set in LabKey Server
##  Note this example expects to find an assay named "SimpleMeans" in the apisamples project
# library(Rlabkey)
simpledf <- labkey.selectRows(
	baseUrl="http://localhost:8080/labkey",
	folderPath="/apisamples",
	schemaName="lists", 
	queryName="AllTypes")

## some dummy calculations to produce and example analysis result
testtable <- simpledf[,3:4]
colnames(testtable) <- c("IntFld", "DoubleFld")
row <- c(list("Measure"="colMeans"), colMeans(testtable, na.rm=TRUE))
results <- data.frame(row, row.names=NULL, stringsAsFactors=FALSE)
row <- c(list("Measure"="colSums"), colSums(testtable, na.rm=TRUE))
results <- rbind(results, as.vector(row))

bprops <- list(LabNotes="this is a simple demo")
bpl <- list(name=paste("Batch ", as.character(date())),properties=bprops) 
rpl <- list(name=paste("Assay Run ", as.character(date())))

assayInfo<- labkey.saveBatch(
	baseUrl="http://localhost:8080/labkey",
	folderPath="/apisamples",
	"SimpleMeans", 
	results, 
	batchPropertyList=bpl,
	runPropertyList=rpl
)