Changes between Version 3 and Version 4 of xQTLBioinformaticianRCheatSheet

Timestamp:

2011-10-27T10:17:03+02:00 (13 years ago)

Author:

jvelde

Comment:

--

xQTLBioinformaticianRCheatSheet

@@ -3 +3 @@
 = [wiki:xQTL xQTL workbench] - Cheat sheet for R scripting =
 
-=== Get a parameter from server ===
-`size <- getparameter("size",jobparams)`
+== Downloading ==
 
-=== Do a status update ===
-`report(2,"Loading 5%...")`
+=== 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")]`
 
-=== Download a data matrix ===
+`find.data()[,c("id","name","investigation","investigation_name")]`
+
+=== Retrieve a data matrix ===
+
 `dataId <- 0`[[BR]]
 `data <- downloadmatrixascsvCURL(dataId)`
 
-=== Upload a completely new data matrix, including annotations ===
+
+== 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]]
@@ -27 +47 @@
 `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]]
+`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%...")`
+
+
+
+