wiki:xQTLBioinformaticianRCheatSheet

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

Annotations, all attributes

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

Annotations, specific attributes

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

Overview of data matrices

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

Data matrix values

dataId <- 0
data <- download.data(dataId)

> Uploading

Annotations

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

New data matrix, plus 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")

File upload

uri <- paste(app_location,"/uploadfile",sep="")
postForm(uri,
name = "example.png",
description = "my plot for experiment x",
investigation_id = "0",
investigation_name = "ClusterDemo",
type = "InvestigationFile",
file = fileUpload(filename = "~/example.png"),
style = "HTTPPOST", curl = .MOLGENIS.curlHandle
)

Automized xQTL analysis

Get a parameter from server

size <- getparameter("size",jobparams)

Do a status update

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

Last modified 4 years ago Last modified on 2012-11-22T13:50:02+01:00