Changeset 462

Timestamp:

06/06/11 12:24:07 (2 years ago)

Author:

nata_courby

Message:

R examples

Location:

trunk/ontoCAT/src/uk/ac/ebi/ontocat

Files:

• examples/R/Example1.R (modified) (2 diffs)
• examples/R/Example2.R (modified) (1 diff)
• examples/R/Example3.R (added)
• examples/R/resources (deleted)
• virtual/LocalisedFileService.java (modified) (2 diffs)

trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/R/Example1.R

@@ -15 +15 @@
 ##########################################################
 # Gene enrichment test by using ontoCAT R package
-# Please use the full version of ontoCAT R package: https://sourceforge.net/projects/ontocat/files/ontoCAT/ontoCAT_R/ontoCAT_1.1.3.tar.gz
+# Please use the full version of ontoCAT R package: https://sourceforge.net/projects/ontocat/files/ontoCAT/ontoCAT_R/ontoCAT_1.1.5.tar.gz
 ##########################################################
+
+#Java Heap size needed to reason over GO ontology (more than 20 MB in size) is 512MB.
+#Here are the instructions how to increase Java Heap Size in R:
+
+library(rJava)
+options(java.parameters="-Xmx512")
+.jinit()
+
+#To check the result:
+.jcall(.jnew("java/lang/Runtime"), "J", "maxMemory")
+#Now it is possible to work with large ontologies like GO
 
 library(RCurl)
@@ -34 +45 @@
 library(ontoCAT)
 
-# Obtain GO slim for biological processes:
-go <- getOntology("http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/R/resources/goslim_bp.obo")
+# Obtain GO ontology
+go <- getOntology("http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo")
 
 # Obtain the list of all GOIDs using biomaRt

trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/R/Example2.R

@@ -15 +15 @@
 ######################################################
 # Search and re-annotation of free-text to ontology
+# Please use the full version of ontoCAT R package: https://sourceforge.net/projects/ontocat/files/ontoCAT/ontoCAT_R/ontoCAT_1.1.5.tar.gz
 ######################################################
+
+#Java Heap size needed to reason over GO ontology (more than 20 MB in size) is 512MB.
+#Here are the instructions how to increase Java Heap Size in R:
+
+library(rJava)
+options(java.parameters="-Xmx512")
+.jinit()
+
+#To check the result:
+.jcall(.jnew("java/lang/Runtime"), "J", "maxMemory")
+#Now it is possible to work with large ontologies like GO
 
 # Table of results of experiments concering morphogenesis, where terms are in free-text form
 results<-data.frame(term=c("sorocarp","endocardium","paraxial mesoderm","embryonic arm","post-embryonic medial fin","mesonephric glomerulus","mesonephric mesenchyme","membranous septum","post-embryonic hindlimb","bronchiole"),value=rnorm(10))
 
-# Obtain GO slim for biological processes
 library(ontoCAT)
-go <- getOntology("http://www.ontocat.org/browser/trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/R/resources/goslim_bp.obo")
+
+# Obtain GO ontology
+go <- getOntology("http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo")
 
 # Re-annotation example using GO ontology

trunk/ontoCAT/src/uk/ac/ebi/ontocat/virtual/LocalisedFileService.java

@@ -56 +56 @@
         /**
          * Instantiates the decorator.
-         * 
+         *
          */
         public LocalisedFileService(FileOntologyService fos) {
@@ -65 +65 @@
         /**
          * Creates the proxy.
-         * 
+         *
          * @param fos
          *            the obj
          *
-         * 
+         *
          * @return the object
          * @throws OntologyServiceException