ClusterPhenoTest        Test association of clusters with phenotype.
ExpressionPhenoTest     Tests univariate association between a list of
                        phenotype variables and gene expression.
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'
epheno                  epheno object.
epheno-class            Class "epheno"
epheno2html             Create html files and plots from an epheno
                        object.
eset                    Example data.
export2CSV              Export object to comma-separated text file.
export2CSV-methods      Methods for Function export2CSV in Package
                        'phenoTest'
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'
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'
htmlpage                htmlpage
pAdjust                 Adjust p values of an epheno object.
pAdjust-methods         Methods for Function pAdjust in Package
                        'phenoTest'
phenoTest-package       Test correlation between gene expression and
                        phenotype.
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.gseaSignificanceSign
                        Obtain a data.frame with the pvalues and fdr
                        for all signatures and variables of a
                        gseaSignificanceSign or gseaSignificanceVar
                        object.
