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phenoTest (version 1.20.0)

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

1.20.0

License

GPL (>=2)

Maintainer

Evarist Planet

Last Published

February 15th, 2017

Functions in phenoTest (1.20.0)

getEsPositions

Obtain chromosome positions for each gene.
gsea

GSEA (Gene Set Enrichment Analysis).
ClusterPhenoTest

Test association of clusters with phenotype.
getVars2test-methods

Methods for Function getVars2test in Package `phenoTest'
get gseaSignatures' elements

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

Class "gseaSignatures" ES and EsSim container.
gsea.kegg

Perform Gene Set Enrichment Analysis (GSEA) of Gene Ontologies (GO) and Kegg gene sets.
eset2genelevel

Filter ExpressionSet to keep one probeset per gene.
gsea2html

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

Methods for Function show in Package `methods'.
epheno

epheno object.
barplotSignatures-methods

Methods for Function barplotSignatures in Package `phenoTest'
epheno2html

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

Class "gseaSignaturesVar"
getVars2test

Get phenotypic variables that were tested.
getKegg

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

Principal components plot.
epheno-class

Class "epheno"
pAdjust-methods

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

Subset an object of class gseaData.
findCopyNumber

Find copy number regions using expression data in a similar way ACE does.
gseaSignificanceSign-class

Class "gseaSignificanceSign"
plot.gseaData

GSEA-like Plot.
export2CSV-methods

Methods for Function export2CSV in Package 'phenoTest'
heatmapPhenoTest

Produce heatmap from phenotype data.
summary.gseaSignificance

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

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

Example data.
eset.genelevel

Example data.
gseaSignatures-methods

Methods for Function gseaSignatures in Package `phenoTest'
heatmapPhenoTest-methods

Methods for Function heatmapPhenoTest in Package `phenoTest'
gseaSignificance

ES' (enrichment scores) sifgnificance.
gseaSignaturesSign-class

Class "gseaSignaturesSign"
write.html

Write a data.frame to an html file.
gseaSignatures

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

Create a list of gene sets based on GO pathways terms.
barplotSignifSignatures-methods

Methods for Function barplotSignifSignatures in Package `phenoTest'
genesInArea

Find genes that are in given areas.
export2CSV

Export object to comma-separated text file.
gseaSignificanceVar-class

Class "gseaSignificanceVar"
phenoTest-package

Test correlation between gene expression and phenotype.
plot.gseaSignatures

GSEA-like Plot.
smoothCoxph

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

Summary plots for gene signature vs phenotype association
pAdjust

Adjust p values of an epheno object.
ExpressionPhenoTest

Tests univariate association between a list of phenotype variables and gene expression.
getters for the epheno object

Getters for the epheno object:
gseaData-class

Class "gseaData"