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.


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Documentation for package ‘phenoTest’ version 1.40.0

Help Pages

phenoTest-package Test correlation between gene expression and phenotype.
approach Getters for the epheno object:
approach-method Class "epheno"
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.
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.
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).
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"
getHr Getters for the epheno object:
getHr-method Class "epheno"
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.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"
heatmapPhenoTest Produce heatmap from phenotype data.
heatmapPhenoTest-method Methods for Function heatmapPhenoTest in Package 'phenoTest'
heatmapPhenoTest-methods Methods for Function heatmapPhenoTest in Package 'phenoTest'
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'
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.
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.
write.html Write a data.frame to an html file.
[-method Class "epheno"
[-method Getters for the epheno object: