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.

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

Author
Evarist Planet
Date of publication
None
Maintainer
Evarist Planet <evarist.planet@epfl.ch>
License
GPL (>=2)
Version
1.20.0

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