# Phenotype Consensus ANalysis (PCAN)

## Documentation for package ‘PCAN’ version 1.12.0

- 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)