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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
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Version
1.0.2
License
CC BY-NC-ND 4.0
Maintainer
Matthew Page
Last Published
March 24th, 2016
Functions in PCAN (1.0.2)
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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)