TracNav(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

Retrieve annotations, all attributes

find.marker()
find.individual()
find.investigation()

Retrieve annotations, specific attributes

find.marker()[,c("name")]
find.individual()[,c("name","investigation_name")]
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
data <- downloadmatrixascsvCURL(dataId)

> Uploading

Add annotations

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

Add a completely new data matrix, including annotations

invId <- 0
data <- NULL
data <- rbind(data, c("A", "B"))
data <- rbind(data, c("B", "A"))
marker1 = add.marker(name="myMarker1", cm="10.0", investigation_id=invId)
marker2 = add.marker(name="myMarker2", cm="20.0", investigation_id=invId)
ind1 = add.individual(name="myInd1", investigation_id=invId)
ind2 = add.individual(name="myInd2", investigation_id=invId)
colnames(data) <- c("myInd1", "myInd2")
rownames(data) <- c("myMarker1", "myMarker2")
add.datamatrix(data, name="myResults", investigation_id=invId, rowtype="Marker", coltype="Individual", valuetype="Text")

Upload a file

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

> Automized xQTL analysis

Get a parameter from server

size <- getparameter("size",jobparams)

Do a status update

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