# OnASSIs Ontology Annotation and Semantic SImilarity software

## Documentation for package ‘Onassis’ version 1.4.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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