Tools to test correlation between gene expression and phenotype.


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Documentation for package ‘phenoTest’ version 1.0.0

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phenoTest-package Test correlation between gene expression and phenotype.
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'
ClusterPhenoTest Test association of clusters with phenotype.
dim-method Class "epheno"
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-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.
getEs Substract element's of a gseaSignaturesSign or gseaSignaturesVar object (obtained using the gseaSignatures function).
getEs-method Class "gseaSignaturesSign"
getEs-method Class "gseaSignaturesVar"
getEsSim Substract element's of a gseaSignaturesSign or gseaSignaturesVar object (obtained using the gseaSignatures function).
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 "gseaSignaturesSign"
getFcHr-method Class "gseaSignaturesVar"
getHr Getters for the epheno object:
getHr-method Class "epheno"
getMeans Getters for the epheno object:
getMeans-method Class "epheno"
getPvals Getters for the epheno object:
getPvals-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'
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"
heatmapPhenoTest Produce heatmap from phenotype data.
heatmapPhenoTest-method Methods for Function heatmapPhenoTest in Package 'phenoTest'
heatmapPhenoTest-methods Methods for Function heatmapPhenoTest in Package 'phenoTest'
htmlpage htmlpage
logFcHr Getters for the epheno object:
logFcHr-method Class "epheno"
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'
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.gseaSignaturesSign GSEA-like Plot.
plot.gseaSignaturesVar GSEA-like Plot.
show-method Class "epheno"
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.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.
[-method Class "epheno"