Phenotype Consensus ANalysis (PCAN)


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Documentation for package ‘PCAN’ version 1.2.1

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calcHpSim Compare HP terms based on semantic similarity
compareHPSets Compare 2 sets of HP terms based on semantic similarity
computeHpIC Compute Information Content (IC) for each HP based on genes by HP
geneByHp Entrez gene IDs associated to HP terms (Example data)
geneByTrait Gene associated to trait (Example data)
geneDef Description of genes (Example data)
hpByTrait HP IDs associated to trait (Example data)
hpDef Description of HP terms (Example data)
hpGeneHeatmap HP to Gene heatmap
hpGeneListComp HP semantic similarity for a whole gene list.
hpSetCompBestMatch Best matches between two sets of HP terms
hpSetCompSummary Global semantic similarity between 2 HP sets
hp_ancestors HP ancestors (Example data)
hp_class HP class (Example data)
hp_descendants HP descendants (Example data)
hqStrNw STRIND database network of Homo sapiens genes (Example data)
hsEntrezByRPath Homo sapiens entrez gene ID by Reactome pathway (Example data)
rPath Reactome pathways (Example data)
traitDef Description of Traits (Example data)