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PCAN (version 1.0.2)

Phenotype Consensus ANalysis (PCAN)

Description

Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).

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Version

Version

1.0.2

License

CC BY-NC-ND 4.0

Maintainer

Matthew Page

Last Published

February 15th, 2017

Functions in PCAN (1.0.2)

traitDef

Description of Traits (Example data)
hp_class

HP class (Example data)
hp_descendants

HP descendants (Example data)
geneDef

Description of genes (Example data)
hpGeneListComp

HP semantic similarity for a whole gene list.
hpByTrait

HP IDs associated to trait (Example data)
hp_ancestors

HP ancestors (Example data)
hsEntrezByRPath

Homo sapiens entrez gene ID by Reactome pathway (Example data)
hpGeneHeatmap

HP to Gene heatmap
hqStrNw

STRIND database network of Homo sapiens genes (Example data)
computeHpIC

Compute Information Content (IC) for each HP based on genes by HP
rPath

Reactome pathways (Example data)
hpDef

Description of HP terms (Example data)
hpSetCompSummary

Global semantic similarity between 2 HP sets
geneByHp

Entrez gene IDs associated to HP terms (Example data)
calcHpSim

Compare HP terms based on semantic similarity
compareHPSets

Compare 2 sets of HP terms based on semantic similarity
hpSetCompBestMatch

Best matches between two sets of HP terms
geneByTrait

Gene associated to trait (Example data)