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phenoTest (version 1.16.0)

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

1.16.0

License

GPL (>=2)

Maintainer

Evarist Planet

Last Published

February 15th, 2017

Functions in phenoTest (1.16.0)

getters for the epheno object

Getters for the epheno object:
ClusterPhenoTest

Test association of clusters with phenotype.
epheno-class

Class "epheno"
export2CSV-methods

Methods for Function export2CSV in Package 'phenoTest'
export2CSV

Export object to comma-separated text file.
gsea2html

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

Class "gseaData"
gseaSignificance

ES' (enrichment scores) sifgnificance.
gseaSignaturesVar-class

Class "gseaSignaturesVar"
eset.genelevel

Example data.
getGo

Create a list of gene sets based on GO pathways terms.
barplotSignatures

Summary plots for gene signature vs phenotype association
show-methods

Methods for Function show in Package `methods'.
get gseaSignatures' elements

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

Principal components plot.
phenoTest-package

Test correlation between gene expression and phenotype.
epheno

epheno object.
epheno2html

Create html files and plots from an epheno object.
gseaSignaturesSign-class

Class "gseaSignaturesSign"
gseaSignificanceSign-class

Class "gseaSignificanceSign"
gseaSignatures

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

Class "gseaSignificanceVar"
summary.gseaData

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

Plots the Cox proportional hazard smoothed by gene expression level.
genesInArea

Find genes that are in given areas.
getEsPositions

Obtain chromosome positions for each gene.
barplotSignifSignatures-methods

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

Methods for Function barplotSignatures in Package `phenoTest'
findCopyNumber

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

Tests univariate association between a list of phenotype variables and gene expression.
gsea.kegg

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

Class "gseaSignatures" ES and EsSim container.
gseaSignatures-methods

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

Subset an object of class gseaData.
pAdjust-methods

Methods for Function pAdjust in Package `phenoTest'
pAdjust

Adjust p values of an epheno object.
summary.gseaSignificance

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

Write a data.frame to an html file.
eset2genelevel

Filter ExpressionSet to keep one probeset per gene.
getVars2test-methods

Methods for Function getVars2test in Package `phenoTest'
getKegg

Create a list of gene sets based on KEGG pathways terms.
eset

Example data.
gsea

GSEA (Gene Set Enrichment Analysis).
getVars2test

Get phenotypic variables that were tested.
heatmapPhenoTest-methods

Methods for Function heatmapPhenoTest in Package `phenoTest'
heatmapPhenoTest

Produce heatmap from phenotype data.
plot.gseaData

GSEA-like Plot.
plot.gseaSignatures

GSEA-like Plot.