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.

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

AuthorEvarist Planet
Date of publicationNone
MaintainerEvarist Planet <evarist.planet@epfl.ch>
LicenseGPL (>=2)
Version1.23.1

View on Bioconductor

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.

Files in this package

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

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