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-methods | Methods for Function barplotSignatures in Package 'phenoTest' |
| barplotSignifSignatures-methods | Methods for Function barplotSignifSignatures in Package... |
| ClusterPhenoTest | Test association of clusters with phenotype. |
| epheno | epheno object. |
| epheno2html | Create html files and plots from an epheno object. |
| epheno-class | Class "epheno" |
| ephenoGetters | Getters for the epheno object: |
| eset | Example data. |
| eset2genelevel | Filter ExpressionSet to keep one probeset per gene. |
| eset.genelevel | Example data. |
| export2CSV | Export object to comma-separated text file. |
| export2CSV-methods | Methods for Function export2CSV in Package 'phenoTest' |
| ExpressionPhenoTest | Tests univariate association between a list of phenotype... |
| findCopyNumber | Find copy number regions using expression data in a similar... |
| genesInArea | Find genes that are in given areas. |
| getEsPositions | Obtain chromosome positions for each gene. |
| getGseaSignatures | Substract element's of a gseaSignaturesSign or... |
| getVars2test | Get phenotypic variables that were tested. |
| getVars2test-methods | Methods for Function getVars2test in Package 'phenoTest' |
| gsea | GSEA (Gene Set Enrichment Analysis). |
| gsea2html | Export an object of class gseaData to an html file. |
| gseaData-class | Class "gseaData" |
| gseaSignatures | Compute ES (enrichment scores) and es.sim (simulated... |
| 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" |
| gsea.subset | Subset an object of class gseaData. |
| heatmapPhenoTest | Produce heatmap from phenotype data. |
| heatmapPhenoTest-methods | Methods for Function heatmapPhenoTest in Package 'phenoTest' |
| pAdjust | Adjust p values of an epheno object. |
| pAdjust-methods | Methods for Function pAdjust in Package 'phenoTest' |
| pca | Principal components plot. |
| phenoTest-package | Test correlation between gene expression and phenotype. |
| plot.gsea | GSEA-like Plot. |
| plot.gseaSignatures | GSEA-like Plot. |
| plots4epheno | Summary plots for gene signature vs phenotype association |
| show-methods | Methods for Function show in Package 'methods'. |
| smoothCoxph | Plots the Cox proportional hazard smoothed by gene expression... |
| summary.gsea | Obtain a data.frame with the pvalues and fdr for all... |
| summary.gseaSignificance | Obtain a data.frame with the pvalues and fdr for all... |
| write.html | Write a data.frame to an html file. |
