PCAN: Phenotype Consensus ANalysis (PCAN)
Version 1.4.0

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).

AuthorMatthew Page and Patrice Godard
Bioconductor views Annotation FunctionalPrediction Genetics Network Pathways Sequencing VariantAnnotation
Date of publicationNone
MaintainerMatthew Page <matthew.page@ucb.com> and Patrice Godard <patrice.godard@gmail.com>
LicenseCC BY-NC-ND 4.0
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PCAN")

Getting started

Assessing gene relevance for a set of phenotypes

Popular man pages

calcHpSim: Compare 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)
hpDef: Description of HP terms (Example data)
hpGeneHeatmap: HP to Gene heatmap
hqStrNw: STRIND database network of Homo sapiens genes (Example data)
rPath: Reactome pathways (Example data)
See all...

All man pages Function index File listing

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)

Functions

calcHpSim Man page Source code
compareHPSets Man page Source code
computeHpIC Man page Source code
geneByHp Man page
geneByTrait Man page
geneDef Man page
hpByTrait Man page
hpDef Man page
hpGeneHeatmap Man page Source code
hpGeneListComp Man page Source code
hpSetCompBestMatch Man page Source code
hpSetCompSummary Man page Source code
hp_ancestors Man page
hp_class Man page
hp_descendants Man page
hqStrNw Man page
hsEntrezByRPath Man page
rPath Man page
traitDef Man page

Files

DESCRIPTION
NAMESPACE
R
R/calcHpSim.R
R/compareHPSets.R
R/computeHpIC.R
R/dataDoc.R
R/hpGeneHeatmap.R
R/hpGeneListComp.R
R/hpSetCompBestMatch.R
R/hpSetCompSummary.R
build
build/vignette.rds
data
data/datalist
data/geneByHp.rda
data/geneByTrait.rda
data/geneDef.rda
data/hpByTrait.rda
data/hpDef.rda
data/hp_ancestors.rda
data/hp_class.rda
data/hp_descendants.rda
data/hqStrNw.rda
data/hsEntrezByRPath.rda
data/rPath.rda
data/traitDef.rda
inst
inst/CITATION
inst/DataPackage-Generator
inst/DataPackage-Generator/Documentation
inst/DataPackage-Generator/Documentation/Data.dia
inst/DataPackage-Generator/Documentation/Data.png
inst/DataPackage-Generator/Documentation/clinvar_public-2015-04-03.xsd
inst/DataPackage-Generator/Package-Template
inst/DataPackage-Generator/Package-Template/DESCRIPTION
inst/DataPackage-Generator/Package-Template/NAMESPACE
inst/DataPackage-Generator/Package-Template/R
inst/DataPackage-Generator/Package-Template/R/MultiPhenoDB.R
inst/DataPackage-Generator/Package-Template/R/zzz.R
inst/DataPackage-Generator/Package-Template/examples
inst/DataPackage-Generator/Package-Template/examples/dataModel.R
inst/DataPackage-Generator/Package-Template/examples/geneAssociations.R
inst/DataPackage-Generator/Package-Template/man
inst/DataPackage-Generator/Package-Template/man/filterGeneByTrait.Rd
inst/DataPackage-Generator/Package-Template/man/getDataModel.Rd
inst/DataPackage-Generator/Package-Template/man/getGeneByHp.Rd
inst/DataPackage-Generator/Package-Template/man/getHpByGene.Rd
inst/DataPackage-Generator/Package-Template/man/mhphdb.con.Rd
inst/DataPackage-Generator/README.txt
inst/DataPackage-Generator/SA00-Gathering-Data.R
inst/DataPackage-Generator/SA01-Reference-Clinical-Variation.R
inst/DataPackage-Generator/SA02-ClinVar.R
inst/DataPackage-Generator/SA03-MedGen.R
inst/DataPackage-Generator/SA04-HP.R
inst/DataPackage-Generator/SA05-Orphanet.R
inst/DataPackage-Generator/SA06-Integration-Semantic-Similarity.R
inst/DataPackage-Generator/SB00-PackageGenerator.R
inst/DataPackage-Generator/clinVar-Functions.R
inst/doc
inst/doc/PCAN.R
inst/doc/PCAN.Rmd
inst/doc/PCAN.html
man
man/calcHpSim.Rd
man/compareHPSets.Rd
man/computeHpIC.Rd
man/geneByHp.Rd
man/geneByTrait.Rd
man/geneDef.Rd
man/hpByTrait.Rd
man/hpDef.Rd
man/hpGeneHeatmap.Rd
man/hpGeneListComp.Rd
man/hpSetCompBestMatch.Rd
man/hpSetCompSummary.Rd
man/hp_ancestors.Rd
man/hp_class.Rd
man/hp_descendants.Rd
man/hqStrNw.Rd
man/hsEntrezByRPath.Rd
man/rPath.Rd
man/traitDef.Rd
vignettes
vignettes/PCAN.Rmd
vignettes/bibliography.bib
PCAN documentation built on May 20, 2017, 10:06 p.m.