OnASSIs Ontology Annotation and Semantic SImilarity software


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Documentation for package ‘Onassis’ version 1.0.1

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A B 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'
annotateDF EntityFinder class to create a Conceptmapper instance
annotateDF-method EntityFinder class to create a Conceptmapper instance
annotateTissueDisease 'annotateTissueDisease'
arguments CMoptions
arguments-method CMoptions
arguments<- CMoptions
arguments<--method CMoptions

-- B --

buildDictionary CMdictionary class that stores a Conceptmapper dictionary
buildDictionary, CMdictionary class that stores a Conceptmapper dictionary
buildDictionary-method CMdictionary class that stores a Conceptmapper dictionary

-- C --

CMdictionary CMdictionary class that stores a Conceptmapper dictionary
CMdictionary-class CMdictionary class that stores a Conceptmapper dictionary
CMdictionary-method CMdictionary class that stores a Conceptmapper dictionary
CMoptions CMoptions
CMoptions-class CMoptions
connectToGEODB 'connectToGEODB'
connectToGEODB, 'connectToGEODB'
connectToSRADB 'connectToSRADB'
create_score_matrix 'createScoreMatrix'

-- D --

dictInfo CMdictionary class that stores a Conceptmapper dictionary
dictInfo, CMdictionary class that stores a Conceptmapper dictionary
dictInfo-method CMdictionary class that stores a Conceptmapper dictionary
dictInfo<- CMdictionary class that stores a Conceptmapper dictionary
dictInfo<-, CMdictionary class that stores a Conceptmapper dictionary
dictInfo<--method CMdictionary class that stores a Conceptmapper dictionary
dictionary CMdictionary class that stores a Conceptmapper dictionary
dictRef CMdictionary class that stores a Conceptmapper dictionary
dictRef, CMdictionary class that stores a Conceptmapper dictionary
dictRef-method CMdictionary class that stores a Conceptmapper dictionary
dictRef<- CMdictionary class that stores a Conceptmapper dictionary
dictRef<-, CMdictionary class that stores a Conceptmapper dictionary
dictRef<--method CMdictionary class that stores a Conceptmapper dictionary
dictTypes CMdictionary class that stores a Conceptmapper dictionary
dictTypes, CMdictionary class that stores a Conceptmapper dictionary
dictTypes-method CMdictionary class that stores a Conceptmapper dictionary
dict_location CMdictionary class that stores a Conceptmapper dictionary
dict_location, CMdictionary class that stores a Conceptmapper dictionary
dict_location-method CMdictionary class that stores a Conceptmapper dictionary
dict_location<- CMdictionary class that stores a Conceptmapper dictionary
dict_location<-, CMdictionary class that stores a Conceptmapper dictionary
dict_location<--method CMdictionary class that stores a Conceptmapper dictionary

-- E --

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

-- F --

filterTerms 'filterTerms'
findEntities EntityFinder class to create a Conceptmapper instance
findEntities-method EntityFinder class to create a Conceptmapper instance
findHealthy 'findHealthy'

-- G --

GEOHandler-function 'connectToGEODB'
getGEOMetadata 'getGEOMetadata'
getSRAMetadata 'getSRAMetadata'
groupConfig Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
groupConfig-method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
groupConfig<- Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
groupConfig<--method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
groupsim Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
groupsim-method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
groupwiseConfigRef Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
groupwiseConfigRef-method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
groupwiseConfigRef<- Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
groupwiseConfigRef<--method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'

-- I --

icConfig Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
icConfig-method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
icConfig<- Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
icConfig<--method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'

-- L --

library_sources 'library_sources'
library_strategies 'library_strategies'
listCombinations CMoptions
listCombinations-method CMoptions

-- M --

multisim Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
multisim-method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'

-- O --

OnASSiS OnASSiS (Ontology Annotations and Semantic Similarity software)
ontology Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
ontology-method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
ontology<- Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
ontology<--method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
organism_types 'organism_types'

-- P --

pairwiseConfig Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
pairwiseConfig-method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
pairwiseConfig<- Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
pairwiseConfig<--method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
pairwiseConfigRef Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
pairwiseConfigRef-method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
pairwiseConfigRef<- Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
pairwiseConfigRef<--method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
paramValueIndex CMoptions
paramValueIndex-method CMoptions
paramValueIndex<- CMoptions
paramValueIndex<--method CMoptions

-- S --

samplesim Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
samplesim-method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
semanticdifference 'semanticdifference'
show-method CMoptions
showOpts Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
showOpts-method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
showSimilarities 'showSimilarities'
sim Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
sim, Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
sim-method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
Similarity Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
similarity Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
Similarity-class Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
Similarity-constructor Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
Similarity-method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
similarityInstance Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
similarityInstance-method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
similarityInstance<- Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'
similarityInstance<--method Similarity class to compute similarities between concepts in ontologies and samples annotated with different concepts 'Similarity-class'

-- T --

typeSystemRef EntityFinder class to create a Conceptmapper instance
typeSystemRef, EntityFinder class to create a Conceptmapper instance
typeSystemRef-method EntityFinder class to create a Conceptmapper instance
typeSystemRef<- EntityFinder class to create a Conceptmapper instance
typeSystemRef<--method EntityFinder class to create a Conceptmapper instance