PCAN: Phenotype Consensus ANalysis (PCAN)

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).

Author
Matthew Page and Patrice Godard
Date of publication
None
Maintainer
Matthew Page <matthew.page@ucb.com> and Patrice Godard <patrice.godard@gmail.com>
License
CC BY-NC-ND 4.0
Version
1.2.0

View on Bioconductor

Man 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...
geneByHp
Entrez gene IDs associated to HP terms (Example data)
geneByTrait
Gene associated to trait (Example data)
geneDef
Description of genes (Example data)
hp_ancestors
HP ancestors (Example data)
hpByTrait
HP IDs associated to trait (Example data)
hp_class
HP class (Example data)
hpDef
Description of HP terms (Example data)
hp_descendants
HP descendants (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
hqStrNw
STRIND database network of Homo sapiens genes (Example data)
hsEntrezByRPath
Homo sapiens entrez gene ID by Reactome pathway (Example...
rPath
Reactome pathways (Example data)
traitDef
Description of Traits (Example data)

Files in this package

PCAN/DESCRIPTION
PCAN/NAMESPACE
PCAN/R
PCAN/R/calcHpSim.R
PCAN/R/compareHPSets.R
PCAN/R/computeHpIC.R
PCAN/R/dataDoc.R
PCAN/R/hpGeneHeatmap.R
PCAN/R/hpGeneListComp.R
PCAN/R/hpSetCompBestMatch.R
PCAN/R/hpSetCompSummary.R
PCAN/build
PCAN/build/vignette.rds
PCAN/data
PCAN/data/datalist
PCAN/data/geneByHp.rda
PCAN/data/geneByTrait.rda
PCAN/data/geneDef.rda
PCAN/data/hpByTrait.rda
PCAN/data/hpDef.rda
PCAN/data/hp_ancestors.rda
PCAN/data/hp_class.rda
PCAN/data/hp_descendants.rda
PCAN/data/hqStrNw.rda
PCAN/data/hsEntrezByRPath.rda
PCAN/data/rPath.rda
PCAN/data/traitDef.rda
PCAN/inst
PCAN/inst/DataPackage-Generator
PCAN/inst/DataPackage-Generator/Documentation
PCAN/inst/DataPackage-Generator/Documentation/Data.dia
PCAN/inst/DataPackage-Generator/Documentation/Data.png
PCAN/inst/DataPackage-Generator/Documentation/clinvar_public-2015-04-03.xsd
PCAN/inst/DataPackage-Generator/Package-Template
PCAN/inst/DataPackage-Generator/Package-Template/DESCRIPTION
PCAN/inst/DataPackage-Generator/Package-Template/NAMESPACE
PCAN/inst/DataPackage-Generator/Package-Template/R
PCAN/inst/DataPackage-Generator/Package-Template/R/MultiPhenoDB.R
PCAN/inst/DataPackage-Generator/Package-Template/R/zzz.R
PCAN/inst/DataPackage-Generator/Package-Template/examples
PCAN/inst/DataPackage-Generator/Package-Template/examples/dataModel.R
PCAN/inst/DataPackage-Generator/Package-Template/examples/geneAssociations.R
PCAN/inst/DataPackage-Generator/Package-Template/man
PCAN/inst/DataPackage-Generator/Package-Template/man/filterGeneByTrait.Rd
PCAN/inst/DataPackage-Generator/Package-Template/man/getDataModel.Rd
PCAN/inst/DataPackage-Generator/Package-Template/man/getGeneByHp.Rd
PCAN/inst/DataPackage-Generator/Package-Template/man/getHpByGene.Rd
PCAN/inst/DataPackage-Generator/Package-Template/man/mhphdb.con.Rd
PCAN/inst/DataPackage-Generator/README.txt
PCAN/inst/DataPackage-Generator/SA00-Gathering-Data.R
PCAN/inst/DataPackage-Generator/SA01-Reference-Clinical-Variation.R
PCAN/inst/DataPackage-Generator/SA02-ClinVar.R
PCAN/inst/DataPackage-Generator/SA03-MedGen.R
PCAN/inst/DataPackage-Generator/SA04-HP.R
PCAN/inst/DataPackage-Generator/SA05-Orphanet.R
PCAN/inst/DataPackage-Generator/SA06-Integration-Semantic-Similarity.R
PCAN/inst/DataPackage-Generator/SB00-PackageGenerator.R
PCAN/inst/DataPackage-Generator/clinVar-Functions.R
PCAN/inst/doc
PCAN/inst/doc/PCAN.R
PCAN/inst/doc/PCAN.Rmd
PCAN/inst/doc/PCAN.html
PCAN/man
PCAN/man/calcHpSim.Rd
PCAN/man/compareHPSets.Rd
PCAN/man/computeHpIC.Rd
PCAN/man/geneByHp.Rd
PCAN/man/geneByTrait.Rd
PCAN/man/geneDef.Rd
PCAN/man/hpByTrait.Rd
PCAN/man/hpDef.Rd
PCAN/man/hpGeneHeatmap.Rd
PCAN/man/hpGeneListComp.Rd
PCAN/man/hpSetCompBestMatch.Rd
PCAN/man/hpSetCompSummary.Rd
PCAN/man/hp_ancestors.Rd
PCAN/man/hp_class.Rd
PCAN/man/hp_descendants.Rd
PCAN/man/hqStrNw.Rd
PCAN/man/hsEntrezByRPath.Rd
PCAN/man/rPath.Rd
PCAN/man/traitDef.Rd
PCAN/vignettes
PCAN/vignettes/PCAN.Rmd
PCAN/vignettes/bibliography.bib