phenoTest: Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.
Version 1.24.0

Tools to test correlation between gene expression and phenotype in a way that is efficient, structured, fast and scalable. GSEA is also provided.

Browse man pages Browse package API and functions Browse package files

AuthorEvarist Planet
Bioconductor views Classification Clustering DifferentialExpression Microarray MultipleComparison
Date of publicationNone
MaintainerEvarist Planet <evarist.planet@epfl.ch>
LicenseGPL (>=2)
Version1.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("phenoTest")

Man pages

barplotSignatures-methods: Methods for Function barplotSignatures in Package 'phenoTest'
barplotSignifSignatures-methods: Methods for Function barplotSignifSignatures in Package...
ClusterPhenoTest: Test association of clusters with phenotype.
epheno: epheno object.
epheno2html: Create html files and plots from an epheno object.
epheno-class: Class "epheno"
ephenoGetters: Getters for the epheno object:
eset: Example data.
eset2genelevel: Filter ExpressionSet to keep one probeset per gene.
eset.genelevel: Example data.
export2CSV: Export object to comma-separated text file.
export2CSV-methods: Methods for Function export2CSV in Package 'phenoTest'
ExpressionPhenoTest: Tests univariate association between a list of phenotype...
findCopyNumber: Find copy number regions using expression data in a similar...
genesInArea: Find genes that are in given areas.
getEsPositions: Obtain chromosome positions for each gene.
getGo: Create a list of gene sets based on GO pathways terms.
getGseaSignatures: Substract element's of a gseaSignaturesSign or...
getKegg: Create a list of gene sets based on KEGG pathways terms.
getVars2test: Get phenotypic variables that were tested.
getVars2test-methods: Methods for Function getVars2test in Package 'phenoTest'
gsea: GSEA (Gene Set Enrichment Analysis).
gsea2html: Export an object of class gseaData to an html file.
gseaData-class: Class "gseaData"
gsea.kegg.go: Perform Gene Set Enrichment Analysis (GSEA) of Gene...
gseaSignatures: Compute ES (enrichment scores) and es.sim (simulated...
gseaSignatures-class: Class "gseaSignatures" ES and EsSim container.
gseaSignatures-methods: Methods for Function gseaSignatures in Package 'phenoTest'
gseaSignaturesSign-class: Class "gseaSignaturesSign"
gseaSignaturesVar-class: Class "gseaSignaturesVar"
gseaSignificance: ES' (enrichment scores) sifgnificance.
gseaSignificanceSign-class: Class "gseaSignificanceSign"
gseaSignificanceVar-class: Class "gseaSignificanceVar"
gsea.subset: Subset an object of class gseaData.
heatmapPhenoTest: Produce heatmap from phenotype data.
heatmapPhenoTest-methods: Methods for Function heatmapPhenoTest in Package 'phenoTest'
pAdjust: Adjust p values of an epheno object.
pAdjust-methods: Methods for Function pAdjust in Package 'phenoTest'
pca: Principal components plot.
phenoTest-package: Test correlation between gene expression and phenotype.
plot.gsea: GSEA-like Plot.
plot.gseaSignatures: GSEA-like Plot.
plots4epheno: Summary plots for gene signature vs phenotype association
show-methods: Methods for Function show in Package 'methods'.
smoothCoxph: Plots the Cox proportional hazard smoothed by gene expression...
summary.gsea: Obtain a data.frame with the pvalues and fdr for all...
summary.gseaSignificance: Obtain a data.frame with the pvalues and fdr for all...
write.html: Write a data.frame to an html file.

Functions

ClusterPhenoTest Man page Source code
ExpressionPhenoTest Man page Source code
[,epheno,ANY,ANY,ANY-method Man page
[,epheno,ANY,ANY-method Man page
approach Man page
approach,epheno-method Man page
barplotCI Source code
barplotSignatures Man page
barplotSignatures,epheno,GeneSet-method Man page
barplotSignatures,epheno,GeneSetCollection-method Man page
barplotSignatures,epheno,character-method Man page
barplotSignatures,epheno,list-method Man page
barplotSignatures-methods Man page
barplotSignifSignatures Man page
barplotSignifSignatures,epheno,GeneSet-method Man page
barplotSignifSignatures,epheno,GeneSetCollection-method Man page
barplotSignifSignatures,epheno,character-method Man page
barplotSignifSignatures,epheno,list-method Man page
barplotSignifSignatures-methods Man page
checkGsetLen Source code
checkGsetSimmetry Source code
dim,epheno-method Man page
enrichmentScore Source code
epheno Man page
epheno-class Man page
epheno2html Man page Source code
eset Man page
eset.genelevel Man page
eset2genelevel Man page Source code
export2CSV Man page
export2CSV,epheno-method Man page
export2CSV-methods Man page
findCopyNumber Man page Source code
genesInArea Man page Source code
getChrWithMedVar Source code
getDistToClosest Source code
getEs Man page
getEs,gseaData-method Man page
getEs,gseaSignaturesSign-method Man page
getEs,gseaSignaturesVar-method Man page
getEsPositions Man page Source code
getEsSim Man page
getEsSim,gseaData-method Man page
getEsSim,gseaSignaturesSign-method Man page
getEsSim,gseaSignaturesVar-method Man page
getEsSimGam Source code
getEsSimulations Source code
getFc Man page
getFc,epheno-method Man page
getFcHr Man page
getFcHr,gseaData-method Man page
getFcHr,gseaSignaturesSign-method Man page
getFcHr,gseaSignaturesVar-method Man page
getGo Man page Source code
getHr Man page
getHr,epheno-method Man page
getIndivPvals Source code
getKegg Man page Source code
getMeans Man page
getMeans,epheno-method Man page
getNes Man page
getNesGam Source code
getNesObs Source code
getNesSim Source code
getNesSimGam Source code
getPostProbs Man page
getPostProbs,epheno-method Man page
getPred Source code
getPvals Man page
getPvals,epheno-method Man page
getRegions Source code
getSignif Man page
getSignif,epheno-method Man page
getSourceData Source code
getSummary Source code
getSummaryDif Man page
getSummaryDif,epheno-method Man page
getVars2test Man page
getVars2test,epheno-method Man page
getVars2test-methods Man page
gsea Man page Source code
gsea.go Man page Source code
gsea.kegg Man page Source code
gsea.selGsets Man page Source code
gsea.selVars Man page Source code
gsea2html Man page Source code
gseaData-class Man page
gseaSignatures Man page
gseaSignatures,ANY,GeneSet-method Man page
gseaSignatures,ANY,character-method Man page
gseaSignatures,epheno,GeneSetCollection-method Man page
gseaSignatures,epheno,list-method Man page
gseaSignatures,matrix,GeneSetCollection-method Man page
gseaSignatures,matrix,list-method Man page
gseaSignatures,numeric,GeneSetCollection-method Man page
gseaSignatures,numeric,list-method Man page
gseaSignatures-class Man page
gseaSignatures-methods Man page
gseaSignaturesSign-class Man page
gseaSignaturesVar-class Man page
gseaSignificance Man page
gseaSignificance,gseaSignaturesSign-method Man page
gseaSignificance,gseaSignaturesVar-method Man page
gseaSignificanceSign-class Man page
gseaSignificanceVar-class Man page
heatmapPhenoTest Man page
heatmapPhenoTest,ExpressionSet,GeneSet-method Man page
heatmapPhenoTest,ExpressionSet,GeneSetCollection-method Man page
heatmapPhenoTest,ExpressionSet,character-method Man page
heatmapPhenoTest,ExpressionSet,list-method Man page
heatmapPhenoTest,ExpressionSet,missing-method Man page
heatmapPhenoTest-methods Man page
libLoaded Source code
logFcHr Man page
logFcHr,epheno-method Man page
p.adjust.method Man page
p.adjust.method,epheno-method Man page
pAdjust Man page
pAdjust,epheno-method Man page
pAdjust-methods Man page
pca Man page Source code
pca.2d Source code
phenoClass Man page
phenoClass,epheno-method Man page
phenoNames Man page
phenoNames,epheno-method Man page
phenoTest Man page
phenoTest-package Man page
plot.gseaData Man page Source code
plot.gseaSignaturesSign Man page Source code
plot.gseaSignaturesVar Man page Source code
plotCopyNumber Source code
plotGSEA Source code
plotGseaPreprocess Source code
preProcess4Ace Source code
preProcessX Source code
qcPlot Source code
rowSD Source code
rowVar Source code
selSignatures Source code
show,ANY-method Man page
show,AnnotatedDataFrame-method Man page
show,LargeDataObject-method Man page
show,MIAME-method Man page
show,MethodDefinition-method Man page
show,MethodSelectionReport-method Man page
show,MethodWithNext-method Man page
show,ObjectsWithPackage-method Man page
show,ScalarCharacter-method Man page
show,ScalarObject-method Man page
show,TestResults-method Man page
show,Versioned-method Man page
show,Versions-method Man page
show,VersionsNull-method Man page
show,classRepresentation-method Man page
show,container-method Man page
show,eSet-method Man page
show,epheno-method Man page
show,genericFunction-method Man page
show,gseaData-method Man page
show,gseaSignaturesSign-method Man page
show,gseaSignaturesVar-method Man page
show,gseaSignificanceSign-method Man page
show,gseaSignificanceVar-method Man page
show,namedList-method Man page
show,oldClass-method Man page
show,signature-method Man page
show,traceable-method Man page
show-methods Man page
smoothCoxph Man page Source code
sortDragHtmlTable Source code
summary.gseaData Man page Source code
summary.gseaSignificanceSign Man page Source code
summary.gseaSignificanceVar Man page Source code
tellNumPerm Source code
write.html Man page Source code

Files

ChangeLog
DESCRIPTION
NAMESPACE
R
R/ClassDefinitions.R
R/epheno.R
R/epheno2html.R
R/epheno_plots.R
R/eset2genelevel.R
R/findCopyNumber.R
R/getGeneSet.R
R/gsea.R
R/gsea2html.R
R/heatmapPhenoTest.R
R/pca.R
R/smoothCoxph.R
R/write.html.R
build
build/vignette.rds
data
data/epheno.RData
data/eset.RData
data/eset.genelevel.RData
inst
inst/doc
inst/doc/phenoTest.R
inst/doc/phenoTest.Rnw
inst/doc/phenoTest.pdf
inst/javascript
inst/javascript/dragtable.js
inst/javascript/sorttable.js
man
man/ClusterPhenoTest.Rd
man/ExpressionPhenoTest.Rd
man/barplotSignatures-methods.Rd
man/barplotSignifSignatures-methods.Rd
man/epheno-class.Rd
man/epheno.Rd
man/epheno2html.Rd
man/ephenoGetters.Rd
man/eset.Rd
man/eset.genelevel.Rd
man/eset2genelevel.Rd
man/export2CSV-methods.Rd
man/export2CSV.Rd
man/findCopyNumber.Rd
man/genesInArea.Rd
man/getEsPositions.Rd
man/getGo.Rd
man/getGseaSignatures.Rd
man/getKegg.Rd
man/getVars2test-methods.Rd
man/getVars2test.Rd
man/gsea.Rd
man/gsea.kegg.go.Rd
man/gsea.subset.Rd
man/gsea2html.Rd
man/gseaData-class.Rd
man/gseaSignatures-class.Rd
man/gseaSignatures-methods.Rd
man/gseaSignatures.Rd
man/gseaSignaturesSign-class.Rd
man/gseaSignaturesVar-class.Rd
man/gseaSignificance.Rd
man/gseaSignificanceSign-class.Rd
man/gseaSignificanceVar-class.Rd
man/heatmapPhenoTest-methods.Rd
man/heatmapPhenoTest.Rd
man/pAdjust-methods.Rd
man/pAdjust.Rd
man/pca.Rd
man/phenoTest-package.Rd
man/plot.gsea.Rd
man/plot.gseaSignatures.Rd
man/plots4epheno.Rd
man/show-methods.Rd
man/smoothCoxph.Rd
man/summary.gsea.Rd
man/summary.gseaSignificance.Rd
man/write.html.Rd
vignettes
vignettes/phenoTest.Rnw
vignettes/references.bib
phenoTest documentation built on May 20, 2017, 10:51 p.m.