barplotSignatures       Summary plots for gene signature vs phenotype
                        association
barplotSignatures-methods
                        Methods for Function barplotSignatures in
                        Package 'phenoTest'
barplotSignifSignatures-methods
                        Methods for Function barplotSignifSignatures in
                        Package 'phenoTest'
ClusterPhenoTest        Test association of clusters with phenotype.
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-methods      Methods for Function export2CSV in Package
                        'phenoTest'
ExpressionPhenoTest     Tests univariate association between a list of
                        phenotype variables and gene expression.
findCopyNumber          Find copy number regions using expression data
                        in a similar way ACE does.
genesInArea             Find genes that are in given areas.
getEs                   Substract element's of a gseaSignaturesSign or
                        gseaSignaturesVar object (obtained using the
                        gseaSignatures function).
getEsPositions          Obtain chromosome positions for each gene.
getFc                   Getters for the epheno object:
getVars2test            Get phenotypic variables that were tested.
getVars2test-methods    Methods for Function getVars2test in Package
                        'phenoTest'
gsea                    GSEA (Gene Set Enrichment Analysis).
gsea.selGsets           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-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"
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.gseaData           GSEA-like Plot.
plot.gseaSignaturesSign
                        GSEA-like Plot.
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.
write.html              Write a data.frame to an html file.
