[[TracNav(xQTL)]]

= [wiki:xQTL xQTL workbench] - Cheat sheet for R scripting =

=== Get a parameter from server ===
`size <- getparameter("size",jobparams)`

=== Do a status update ===
`report(2,"Loading 5%...")`

=== Get a simple overview of all data matrices ===
`find.data()[,c("id","name")]`

=== Download a data matrix ===
`dataId <- 0`[[BR]]
`data <- downloadmatrixascsvCURL(dataId)`

=== Upload a completely new data matrix, including annotations ===
`invId <- 0`[[BR]]
`data <- NULL`[[BR]]
`data <- rbind(data, c("A", "B"))`[[BR]]
`data <- rbind(data, c("B", "A"))`[[BR]]
`marker1 = add.marker(name="myMarker1", cm="10.0", investigation_id=invId)`[[BR]]
`marker2 = add.marker(name="myMarker2", cm="20.0", investigation_id=invId)`[[BR]]
`ind1 = add.individual(name="myInd1", investigation_id=invId)`[[BR]]
`ind2 = add.individual(name="myInd2", investigation_id=invId)`[[BR]]
`colnames(data) <- c("myInd1", "myInd2")`[[BR]]
`rownames(data) <- c("myMarker1", "myMarker2")`[[BR]]
`add.datamatrix(data, name="myResults", investigation_id=invId, rowtype="Marker", coltype="Individual", valuetype="Text")`[[BR]]

=== Upload a file ===
`uri <- paste(dbpath,"/uploadfile",sep="")`[[BR]]
`path <- "testimage.png"`[[BR]]
`postForm(uri,investigation_name=investigationname, name="my_image", type="InvestigationFile", file=fileUpload(filename=path), style='HTTPPOST')`