[[TracNav(xQTL)]]

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

== Downloading ==

=== Retrieve annotations, all attributes ===

`find.marker()`[[BR]]
`find.individual()`[[BR]]
`find.investigation()`

=== Retrieve annotations, specific attributes ===

`find.marker()[,c("name")]`[[BR]]
`find.individual()[,c("name","investigation_name")]`[[BR]]
`find.investigation()[,c("id","name")]`

=== Get a simple overview of all data matrices ===

`find.data()[,c("id","name","investigation","investigation_name")]`

=== Retrieve a data matrix ===

`dataId <- 0`[[BR]]
`data <- downloadmatrixascsvCURL(dataId)`


== Uploading ==

=== Add annotations ===

`invId <- 0`[[BR]]
`add.individual(name="testIndv", investigation_id=invId)`[[BR]]
`add.marker(name="testMarker2", cm="11.3", bpstart="456237", investigation_id=invId)`

=== Add 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")`

=== 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')`

== Automized xQTL analysis ==

=== Get a parameter from server ===

`size <- getparameter("size",jobparams)`

=== Do a status update ===

`report(2,"Loading 5%...")`