source: trunk/ontoCAT/src/uk/ac/ebi/ontocat/examples/R/Example2.R @ 464

#   Copyright (c) 2010 - 2011 European Molecular Biology Laboratory
#
#   Licensed under the Apache License, Version 2.0 (the "License");
#   you may not use this file except in compliance with the License.
#   You may obtain a copy of the License at
#
#       http://www.apache.org/licenses/LICENSE-2.0
#
#   Unless required by applicable law or agreed to in writing, software
#   distributed under the License is distributed on an "AS IS" BASIS,
#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#   See the License for the specific language governing permissions and
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######################################################
# 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_1.2.1.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))

library(ontoCAT)

# Obtain GO ontology
go <- getOntology("http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo")

# Re-annotation example using GO ontology
annotations<-c(lapply(results$term,function(x) searchTerm(go, paste(x, "morphogenesis", sep=" "))),recursive = TRUE)

results$GOID <- annotations