Man pages for phenoTest
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.

barplotSignatures-methodsMethods for Function barplotSignatures in Package 'phenoTest'
barplotSignifSignatures-methodsMethods for Function barplotSignifSignatures in Package...
ClusterPhenoTestTest association of clusters with phenotype.
ephenoepheno object.
epheno2htmlCreate html files and plots from an epheno object.
epheno-classClass "epheno"
ephenoGettersGetters for the epheno object:
esetExample data.
eset2genelevelFilter ExpressionSet to keep one probeset per gene.
eset.genelevelExample data.
export2CSVExport object to comma-separated text file.
export2CSV-methodsMethods for Function export2CSV in Package 'phenoTest'
ExpressionPhenoTestTests univariate association between a list of phenotype...
findCopyNumberFind copy number regions using expression data in a similar...
genesInAreaFind genes that are in given areas.
getEsPositionsObtain chromosome positions for each gene.
getGoCreate a list of gene sets based on GO pathways terms.
getGseaSignaturesSubstract element's of a gseaSignaturesSign or...
getKeggCreate a list of gene sets based on KEGG pathways terms.
getVars2testGet phenotypic variables that were tested.
getVars2test-methodsMethods for Function getVars2test in Package 'phenoTest'
gseaGSEA (Gene Set Enrichment Analysis).
gsea2htmlExport an object of class gseaData to an html file.
gseaData-classClass "gseaData"
gsea.kegg.goPerform Gene Set Enrichment Analysis (GSEA) of Gene...
gseaSignaturesCompute ES (enrichment scores) and es.sim (simulated...
gseaSignatures-classClass "gseaSignatures" ES and EsSim container.
gseaSignatures-methodsMethods for Function gseaSignatures in Package 'phenoTest'
gseaSignaturesSign-classClass "gseaSignaturesSign"
gseaSignaturesVar-classClass "gseaSignaturesVar"
gseaSignificanceES' (enrichment scores) sifgnificance.
gseaSignificanceSign-classClass "gseaSignificanceSign"
gseaSignificanceVar-classClass "gseaSignificanceVar"
gsea.subsetSubset an object of class gseaData.
heatmapPhenoTestProduce heatmap from phenotype data.
heatmapPhenoTest-methodsMethods for Function heatmapPhenoTest in Package 'phenoTest'
pAdjustAdjust p values of an epheno object.
pAdjust-methodsMethods for Function pAdjust in Package 'phenoTest'
pcaPrincipal components plot.
phenoTest-packageTest correlation between gene expression and phenotype.
plot.gseaGSEA-like Plot.
plot.gseaSignaturesGSEA-like Plot.
plots4ephenoSummary plots for gene signature vs phenotype association
show-methodsMethods for Function show in Package 'methods'.
smoothCoxphPlots the Cox proportional hazard smoothed by gene expression...
summary.gseaObtain a data.frame with the pvalues and fdr for all...
summary.gseaSignificanceObtain a data.frame with the pvalues and fdr for all...
write.htmlWrite a data.frame to an html file.
phenoTest documentation built on May 2, 2018, 3:15 a.m.