# 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.

## Documentation for package ‘phenoTest’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H L P S W misc

phenoTest-package | Test correlation between gene expression and phenotype.

## -- A --

approach | Getters for the epheno object:
approach-method | Class "epheno"

## -- B --

barplotSignatures | Summary plots for gene signature vs phenotype association
barplotSignatures-method | Methods for Function barplotSignatures in Package 'phenoTest'
barplotSignatures-methods | Methods for Function barplotSignatures in Package 'phenoTest'
barplotSignifSignatures | Summary plots for gene signature vs phenotype association
barplotSignifSignatures-method | Methods for Function barplotSignifSignatures in Package 'phenoTest'
barplotSignifSignatures-methods | Methods for Function barplotSignifSignatures in Package 'phenoTest'

## -- C --

ClusterPhenoTest | Test association of clusters with phenotype.

## -- D --

dim-method | Class "epheno"

## -- E --

epheno | epheno object.
epheno-class | Class "epheno"
epheno2html | Create html files and plots from an epheno object.
eset | Example data.
eset.genelevel | Example data.
eset2genelevel | Filter ExpressionSet to keep one probeset per gene.
export2CSV | Export object to comma-separated text file.
export2CSV-method | Methods for Function export2CSV in Package 'phenoTest'
export2CSV-methods | Methods for Function export2CSV in Package 'phenoTest'
ExpressionPhenoTest | Tests univariate association between a list of phenotype variables and gene expression.

## -- F --

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

## -- G --

genesInArea | Find genes that are in given areas.
getEs | Substract element's of a gseaSignaturesSign or gseaSignaturesVar object (obtained using the gseaSignatures function).
getEs-method | Class "gseaData"
getEs-method | Class "gseaSignaturesSign"
getEs-method | Class "gseaSignaturesVar"
getEsPositions | Obtain chromosome positions for each gene.
getEsSim | Substract element's of a gseaSignaturesSign or gseaSignaturesVar object (obtained using the gseaSignatures function).
getEsSim-method | Class "gseaData"
getEsSim-method | Class "gseaSignaturesSign"
getEsSim-method | Class "gseaSignaturesVar"
getFc | Getters for the epheno object:
getFc-method | Class "epheno"
getFcHr | Substract element's of a gseaSignaturesSign or gseaSignaturesVar object (obtained using the gseaSignatures function).
getFcHr-method | Class "gseaData"
getFcHr-method | Class "gseaSignaturesSign"
getFcHr-method | Class "gseaSignaturesVar"
getGo | Create a list of gene sets based on GO pathways terms.
getHr | Getters for the epheno object:
getHr-method | Class "epheno"
getKegg | Create a list of gene sets based on KEGG pathways terms.
getMeans | Getters for the epheno object:
getMeans-method | Class "epheno"
getNes | Substract element's of a gseaSignaturesSign or gseaSignaturesVar object (obtained using the gseaSignatures function).
getPostProbs | Getters for the epheno object:
getPostProbs-method | Class "epheno"
getPvals | Getters for the epheno object:
getPvals-method | Class "epheno"
getSignif | Getters for the epheno object:
getSignif-method | Class "epheno"
getSummaryDif | Getters for the epheno object:
getSummaryDif-method | Class "epheno"
getVars2test | Get phenotypic variables that were tested.
getVars2test-method | Methods for Function getVars2test in Package 'phenoTest'
getVars2test-methods | Methods for Function getVars2test in Package 'phenoTest'
gsea | GSEA (Gene Set Enrichment Analysis).
gsea.go | Perform Gene Set Enrichment Analysis (GSEA) of Gene Ontologies (GO) and Kegg gene sets.
gsea.kegg | Perform Gene Set Enrichment Analysis (GSEA) of Gene Ontologies (GO) and Kegg gene sets.
gsea.selGsets | Subset an object of class gseaData.
gsea.selVars | Subset an object of class gseaData.
gsea2html | Export an object of class gseaData to an html file.
gseaData-class | Class "gseaData"
gseaSignatures | Compute ES (enrichment scores) and es.sim (simulated enrichment scores) for given phenotipic variable(s) and signature(s).
gseaSignatures-class | Class "gseaSignatures" ES and EsSim container.
gseaSignatures-method | Methods for Function gseaSignatures in Package 'phenoTest'
gseaSignatures-methods | Methods for Function gseaSignatures in Package 'phenoTest'
gseaSignaturesSign-class | Class "gseaSignaturesSign"
gseaSignaturesVar-class | Class "gseaSignaturesVar"
gseaSignificance | ES' (enrichment scores) sifgnificance.
gseaSignificance-method | Class "gseaSignaturesSign"
gseaSignificance-method | Class "gseaSignaturesVar"
gseaSignificanceSign-class | Class "gseaSignificanceSign"
gseaSignificanceVar-class | Class "gseaSignificanceVar"

## -- H --

heatmapPhenoTest | Produce heatmap from phenotype data.
heatmapPhenoTest-method | Methods for Function heatmapPhenoTest in Package 'phenoTest'
heatmapPhenoTest-methods | Methods for Function heatmapPhenoTest in Package 'phenoTest'

## -- L --

logFcHr | Getters for the epheno object:
logFcHr-method | Class "epheno"

## -- P --

p.adjust.method | Getters for the epheno object:
p.adjust.method-method | Class "epheno"
pAdjust | Adjust p values of an epheno object.
pAdjust-method | Methods for Function pAdjust in Package 'phenoTest'
pAdjust-methods | Methods for Function pAdjust in Package 'phenoTest'
pca | Principal components plot.
phenoClass | Getters for the epheno object:
phenoClass-method | Class "epheno"
phenoNames | Getters for the epheno object:
phenoNames-method | Class "epheno"
phenoTest | Test correlation between gene expression and phenotype.
plot.gseaData | GSEA-like Plot.
plot.gseaSignaturesSign | GSEA-like Plot.
plot.gseaSignaturesVar | GSEA-like Plot.

## -- S --

show-method | Class "epheno"
show-method | Class "gseaData"
show-method | Methods for Function show in Package 'methods'.
show-methods | Methods for Function show in Package 'methods'.
smoothCoxph | Plots the Cox proportional hazard smoothed by gene expression level.
summary.gseaData | Obtain a data.frame with the pvalues and fdr for all signatures and variables of a gseaData object.
summary.gseaSignificanceSign | Obtain a data.frame with the pvalues and fdr for all signatures and variables of a gseaSignificanceSign or gseaSignificanceVar object.
summary.gseaSignificanceVar | Obtain a data.frame with the pvalues and fdr for all signatures and variables of a gseaSignificanceSign or gseaSignificanceVar object.

## -- W --

write.html | Write a data.frame to an html file.

## -- misc --

[-method | Class "epheno"
[-method | Getters for the epheno object: