Phenotype Consensus ANalysis (PCAN)

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Documentation for package ‘PCAN’ version 1.33.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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)