GO-terms Semantic Similarity Measures


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Documentation for package ‘GOSemSim’ version 1.14.0

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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"
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"