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 1.40.0

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: