OnASSIs Ontology Annotation and Semantic SImilarity software

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Documentation for package ‘Onassis’ version 1.2.7

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A C D E F G I L M O P S T

OnASSiS-package OnASSiS (Ontology Annotations and Semantic Similarity software)
Onassis-package OnASSiS (Ontology Annotations and Semantic Similarity software)

-- A --

annotate 'annotate'
annotate-method 'annotate'
annotateDF 'annotateDF'
annotateDF-method 'annotateDF'
annotateTissueDisease 'annotateTissueDisease'

-- C --

CaseMatch 'CaseMatch'
CaseMatch-method 'CaseMatch'
CaseMatch<- 'CaseMatch'
CaseMatch<--method 'CaseMatch'
CMdictionary 'CMdictionary'
CMdictionary-class Class that stores a Conceptmapper dictionary
CMoptions 'CMoptions'
CMoptions-class Class to set the options to run the EntityFinder
collapse 'collapse'
collapse-method 'collapse'
compare 'compare'
compare-method 'compare'
connectToGEODB 'connectToGEODB'
connectToGEODB, 'connectToGEODB'
create_score_matrix 'createScoreMatrix'

-- D --

dictInfo Get and Set the dicInfo slot for the 'CMdictionary' class
dictInfo-method Get and Set the dicInfo slot for the 'CMdictionary' class
dictInfo<- Get and Set the dicInfo slot for the 'CMdictionary' class
dictInfo<--method Get and Set the dicInfo slot for the 'CMdictionary' class
dictionary 'dictionary<-'
dictionary-method 'dictionary<-'
dictionary<- 'dictionary<-'
dictionary<--method 'dictionary<-'
dictRef 'dictRef'
dictRef-method 'dictRef'
dictRef<- 'dictRef'
dictRef<--method 'dictRef'
dictTypes 'dictTypes'
dict_location 'dict_location'
dict_location-method 'dict_location'
dict_location<- 'dict_location'
dict_location<--method 'dict_location'

-- E --

entities 'entities<-'
entities-method 'entities<-'
entities<- 'entities<-'
entities<--method 'entities<-'
EntityFinder 'EntityFinder'
EntityFinder-class EntityFinder class to create a Conceptmapper instance
experiment_types 'experiment_types'

-- F --

filterconcepts 'filterconcepts'
filterconcepts-method 'filterconcepts'
filterTerms 'filterTerms'
FindAllMatches Method FindAllMatches
FindAllMatches-method Method FindAllMatches
FindAllMatches<- Method FindAllMatches
FindAllMatches<--method Method FindAllMatches
findEntities Method findEntities
findEntities-method Method findEntities
findHealthy 'findHealthy'

-- G --

GEOHandler-function 'connectToGEODB'
getGEOMetadata 'getGEOMetadata'
groupConfig 'groupConfig'
groupConfig-method 'groupConfig'
groupConfig<- 'groupConfig'
groupConfig<--method 'groupConfig'
groupsim Method groupsim
groupsim-method Method groupsim
groupwiseConfigRef 'groupwiseConfigRef'
groupwiseConfigRef-method 'groupwiseConfigRef'
groupwiseConfigRef<- 'groupwiseConfigRef'
groupwiseConfigRef<--method 'groupwiseConfigRef'

-- I --

icConfig 'icConfig'
icConfig-method 'icConfig'
icConfig<- 'icConfig'
icConfig<--method 'icConfig'

-- L --

listCMOptions 'listCMOptions'
listSimilarities 'listSimilarities'

-- M --

mergeonassis 'mergeonassis'
mergeonassis-method 'mergeonassis'
multisim 'multisim'
multisim-method 'multisim'

-- O --

OnASSiS OnASSiS (Ontology Annotations and Semantic Similarity software)
Onassis OnASSiS (Ontology Annotations and Semantic Similarity software)
Onassis-class Onassis-class
ontology 'ontology<-'
ontology-method 'ontology<-'
ontology<- 'ontology<-'
ontology<--method 'ontology<-'
OrderIndependentLookup 'OrderIndependentLookup'
OrderIndependentLookup-method 'OrderIndependentLookup'
OrderIndependentLookup<- 'OrderIndependentLookup'
OrderIndependentLookup<--method 'OrderIndependentLookup'
organism_types 'organism_types'

-- P --

pairsim 'pairsim'
pairsim-method 'pairsim'
pairwiseConfig 'pairwiseConfig'
pairwiseConfig-method 'pairwiseConfig'
pairwiseConfig<- 'pairwiseConfig'
pairwiseConfig<--method 'pairwiseConfig'
pairwiseConfigRef 'pairwiseConfigRef'
pairwiseConfigRef-method 'pairwiseConfigRef'
pairwiseConfigRef<- 'pairwiseConfigRef'
pairwiseConfigRef<--method 'pairwiseConfigRef'
paramValueIndex Method paramValueIndex
paramValueIndex-method Method paramValueIndex
paramValueIndex<- Method paramValueIndex
paramValueIndex<--method Method paramValueIndex

-- S --

samplesim 'samplesim'
samplesim-method 'samplesim'
scores 'scores<-'
scores-method 'scores<-'
scores<- 'scores<-'
scores<--method 'scores<-'
SearchStrategy Method SearchStrategy
SearchStrategy-method Method SearchStrategy
SearchStrategy<- Method SearchStrategy
SearchStrategy<--method Method SearchStrategy
semanticdifference 'semanticdifference'
show-method Class to set the options to run the EntityFinder
sim 'sim'
sim-method 'sim'
simil 'simil<-'
simil-method 'simil<-'
simil<- 'simil<-'
simil<--method 'simil<-'
Similarity 'Similarity'
Similarity-class Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
similarityInstance 'similarityInstance'
similarityInstance-method 'similarityInstance'
similarityInstance<- 'similarityInstance'
similarityInstance<--method 'similarityInstance'
Stemmer Method Stemmer
Stemmer-method Method Stemmer
Stemmer<- Method Stemmer
Stemmer<--method Method Stemmer
StopWords Method StopWords
StopWords-method Method StopWords
StopWords<- Method StopWords
StopWords<--method Method StopWords
SynonymType Method SynonymType
SynonymType-method Method SynonymType
SynonymType<- Method SynonymType
SynonymType<--method Method SynonymType

-- T --

typeSystemRef Method typeSystemRef
typeSystemRef-method Method typeSystemRef
typeSystemRef<- Method typeSystemRef
typeSystemRef<--method Method typeSystemRef