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phenoTest (version 1.18.0)

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.

Description

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

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Version

Version

1.18.0

License

GPL (>=2)

Maintainer

Evarist Planet

Last Published

February 15th, 2017

Functions in phenoTest (1.18.0)

eset.genelevel

Example data.
epheno2html

Create html files and plots from an epheno object.
eset

Example data.
barplotSignifSignatures-methods

Methods for Function barplotSignifSignatures in Package `phenoTest'
barplotSignatures-methods

Methods for Function barplotSignatures in Package `phenoTest'
getters for the epheno object

Getters for the epheno object:
epheno

epheno object.
ClusterPhenoTest

Test association of clusters with phenotype.
epheno-class

Class "epheno"
eset2genelevel

Filter ExpressionSet to keep one probeset per gene.
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 variables and gene expression.
getKegg

Create a list of gene sets based on KEGG pathways terms.
getVars2test-methods

Methods for Function getVars2test in Package `phenoTest'
getEsPositions

Obtain chromosome positions for each gene.
getGo

Create a list of gene sets based on GO pathways terms.
get gseaSignatures' elements

Substract element's of a gseaSignaturesSign or gseaSignaturesVar object (obtained using the gseaSignatures function).
findCopyNumber

Find copy number regions using expression data in a similar way ACE does.
genesInArea

Find genes that are in given areas.
gseaSignatures

Compute ES (enrichment scores) and es.sim (simulated enrichment scores) for given phenotipic variable(s) and signature(s).
smoothCoxph

Plots the Cox proportional hazard smoothed by gene expression level.
gseaSignaturesSign-class

Class "gseaSignaturesSign"
gseaSignificanceVar-class

Class "gseaSignificanceVar"
gseaSignificanceSign-class

Class "gseaSignificanceSign"
gseaSignatures-class

Class "gseaSignatures" ES and EsSim container.
summary.gseaData

Obtain a data.frame with the pvalues and fdr for all signatures and variables of a gseaData object.
gseaSignatures-methods

Methods for Function gseaSignatures in Package `phenoTest'
gseaSignaturesVar-class

Class "gseaSignaturesVar"
gseaSignificance

ES' (enrichment scores) sifgnificance.
show-methods

Methods for Function show in Package `methods'.
gsea.kegg

Perform Gene Set Enrichment Analysis (GSEA) of Gene Ontologies (GO) and Kegg gene sets.
pAdjust-methods

Methods for Function pAdjust in Package `phenoTest'
gsea.selGsets

Subset an object of class gseaData.
pAdjust

Adjust p values of an epheno object.
barplotSignatures

Summary plots for gene signature vs phenotype association
gseaData-class

Class "gseaData"
gsea2html

Export an object of class gseaData to an html file.
pca

Principal components plot.
phenoTest-package

Test correlation between gene expression and phenotype.
getVars2test

Get phenotypic variables that were tested.
gsea

GSEA (Gene Set Enrichment Analysis).
summary.gseaSignificance

Obtain a data.frame with the pvalues and fdr for all signatures and variables of a gseaSignificanceSign or gseaSignificanceVar object.
heatmapPhenoTest

Produce heatmap from phenotype data.
write.html

Write a data.frame to an html file.
plot.gseaData

GSEA-like Plot.
heatmapPhenoTest-methods

Methods for Function heatmapPhenoTest in Package `phenoTest'
plot.gseaSignatures

GSEA-like Plot.