[[TracNav(xQTL)]]

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

Start off by connecting R to your application database. Click '''R api''' in the top right corner and copy-paste the content into an R terminal. The R API is usually available under !http://{myhost}/{myapplication}/api/R/. You can now use the following commands:

== > Downloading ==

=== Annotations, all attributes ===

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

=== Annotations, specific attributes ===

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

=== Overview of data matrices ===

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

=== Data matrix values ===

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


== > Uploading ==

=== Annotations ===

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

=== New data matrix, plus 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")`

=== File ===

`uri <- paste(serverpath,"/uploadfile",sep="")`[[BR]]
`postForm(uri,`[[BR]]
` name = "celegan.jpg",`[[BR]]
` Investigation_name = "Studie9_10",`[[BR]]
` type = "InvestigationFile",`[[BR]]
` file = fileUpload(filename = "~/celegan.jpg"),`[[BR]]
` style = "HTTPPOST"`[[BR]]
`)`

== > Automized xQTL analysis ==

=== Get a parameter from server ===

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

=== Do a status update ===

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