GO-terms Semantic Similarity Measures

Documentation for package ‘GOSemSim’ version 1.12.1

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GOSemSim-package	Gene Ontology-based Sematic Similarity Measures
clusterSim	Semantic Similarity Between Two Gene Clusters
computeIC	Class "Params"
computeIC-method	Class "Params"
GeneClusterSet-class	Class "GeneClusterSet"
GeneSet-class	Class "GeneSet"
geneSim	Semantic Similarity Between two Genes
GOSemSim	Gene Ontology-based Sematic Similarity Measures
GOSet	Methods for GOSet class
GOSet-class	Class "GOSet"
GOSet-methods	Methods for GOSet class
goSim	Semantic Similarity Between Two GO Terms
IC	Information content of GO terms
Info_Contents_anopheles_BP	Information content of GO terms
Info_Contents_anopheles_CC	Information content of GO terms
Info_Contents_anopheles_MF	Information content of GO terms
Info_Contents_arabidopsis_BP	Information content of GO terms
Info_Contents_arabidopsis_CC	Information content of GO terms
Info_Contents_arabidopsis_MF	Information content of GO terms
Info_Contents_bovine_BP	Information content of GO terms
Info_Contents_bovine_CC	Information content of GO terms
Info_Contents_bovine_MF	Information content of GO terms
Info_Contents_canine_BP	Information content of GO terms
Info_Contents_canine_CC	Information content of GO terms
Info_Contents_canine_MF	Information content of GO terms
Info_Contents_chicken_BP	Information content of GO terms
Info_Contents_chicken_CC	Information content of GO terms
Info_Contents_chicken_MF	Information content of GO terms
Info_Contents_chimp_BP	Information content of GO terms
Info_Contents_chimp_CC	Information content of GO terms
Info_Contents_chimp_MF	Information content of GO terms
Info_Contents_coelicolor_BP	Information content of GO terms
Info_Contents_coelicolor_CC	Information content of GO terms
Info_Contents_coelicolor_MF	Information content of GO terms
Info_Contents_ecolik12_BP	Information content of GO terms
Info_Contents_ecolik12_CC	Information content of GO terms
Info_Contents_ecolik12_MF	Information content of GO terms
Info_Contents_ecsakai_BP	Information content of GO terms
Info_Contents_ecsakai_CC	Information content of GO terms
Info_Contents_ecsakai_MF	Information content of GO terms
Info_Contents_fly_BP	Information content of GO terms
Info_Contents_fly_CC	Information content of GO terms
Info_Contents_fly_MF	Information content of GO terms
Info_Contents_human_BP	Information content of GO terms
Info_Contents_human_CC	Information content of GO terms
Info_Contents_human_MF	Information content of GO terms
Info_Contents_malaria_BP	Information content of GO terms
Info_Contents_malaria_CC	Information content of GO terms
Info_Contents_malaria_MF	Information content of GO terms
Info_Contents_mouse_BP	Information content of GO terms
Info_Contents_mouse_CC	Information content of GO terms
Info_Contents_mouse_MF	Information content of GO terms
Info_Contents_pig_BP	Information content of GO terms
Info_Contents_pig_CC	Information content of GO terms
Info_Contents_pig_MF	Information content of GO terms
Info_Contents_rat_BP	Information content of GO terms
Info_Contents_rat_CC	Information content of GO terms
Info_Contents_rat_MF	Information content of GO terms
Info_Contents_rhesus_BP	Information content of GO terms
Info_Contents_rhesus_CC	Information content of GO terms
Info_Contents_rhesus_MF	Information content of GO terms
Info_Contents_worm_BP	Information content of GO terms
Info_Contents_worm_CC	Information content of GO terms
Info_Contents_worm_MF	Information content of GO terms
Info_Contents_xenopus_BP	Information content of GO terms
Info_Contents_xenopus_CC	Information content of GO terms
Info_Contents_xenopus_MF	Information content of GO terms
Info_Contents_yeast_BP	Information content of GO terms
Info_Contents_yeast_CC	Information content of GO terms
Info_Contents_yeast_MF	Information content of GO terms
Info_Contents_zebrafish_BP	Information content of GO terms
Info_Contents_zebrafish_CC	Information content of GO terms
Info_Contents_zebrafish_MF	Information content of GO terms
loadAnnoPkg	Class "Params"
loadAnnoPkg-method	Class "Params"
loadGOMap	Class "Params"
loadGOMap-method	Class "Params"
loadICdata	Class "Params"
loadICdata-method	Class "Params"
mclusterSim	Pairwise Semantic Similarities for a List of Gene Clusters
mgeneSim	Pairwise Semantic Similarity for a List of Genes
mgoSim	Semantic Similarity Between two GO terms lists
Params	Methods for Params class
Params-class	Class "Params"
Params-methods	Methods for Params class
setCombineMethod<-	Class "Params"
setCombineMethod<--method	Class "Params"
setMethod<-	Class "Params"
setMethod<--method	Class "Params"
setOntology<-	Class "Params"
setOntology<--method	Class "Params"
setOrganism<-	Class "Params"
setOrganism<--method	Class "Params"
sim	Methods for calculating semantic similarity
sim-method	Methods for calculating semantic similarity
sim-methods	Methods for calculating semantic similarity
[-method	Class "Params"