Package: phenoTest 1.55.0
Evarist Planet
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.
Tools to test correlation between gene expression and phenotype in a way that is efficient, structured, fast and scalable. GSEA is also provided.
Authors:
phenoTest_1.55.0.tar.gz
phenoTest_1.55.0.zip(r-4.5)phenoTest_1.55.0.zip(r-4.4)phenoTest_1.55.0.zip(r-4.3)
phenoTest_1.55.0.tgz(r-4.4-any)phenoTest_1.55.0.tgz(r-4.3-any)
phenoTest_1.55.0.tar.gz(r-4.5-noble)phenoTest_1.55.0.tar.gz(r-4.4-noble)
phenoTest_1.55.0.tgz(r-4.4-emscripten)phenoTest_1.55.0.tgz(r-4.3-emscripten)
phenoTest.pdf |phenoTest.html✨
phenoTest/json (API)
| # Install 'phenoTest' in R: |
| install.packages('phenoTest', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- epheno - Epheno object.
- eset - Example data.
- eset.genelevel - Example data.
On BioConductor:phenoTest-1.55.0(bioc 3.21)phenoTest-1.54.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarraydifferentialexpressionmultiplecomparisonclusteringclassification
Last updated 20 days agofrom:689f101f10. Checks:OK: 1 NOTE: 4 WARNING: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 31 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | WARNING | Oct 31 2024 |
| R-4.3-mac | WARNING | Oct 31 2024 |
Exports:approachbarplotSignaturesbarplotSignifSignaturesClusterPhenoTestepheno2htmleset2genelevelexport2CSVExpressionPhenoTestfindCopyNumbergenesInAreagetEsgetEsPositionsgetEsSimgetFcgetFcHrgetHrgetMeansgetPostProbsgetPvalsgetSignifgetSummaryDifgetVars2testgseagsea.selGsetsgsea.selVarsgsea2htmlgseaSignaturesgseaSignificanceheatmapPhenoTestlogFcHrp.adjust.methodpAdjustpcaphenoClassphenoNamesplot.gseaDataplot.gseaSignaturesSignplot.gseaSignaturesVarshowsmoothCoxphsummary.gseaDatasummary.gseaSignificanceSignsummary.gseaSignificanceVarwrite.html
Dependencies:annotateAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64bitopsblobBMAbslibcachemCategorycaToolscheckmatecliclustercolorspacecpp11crayoncurldata.tableDBIdbplyrDEoptimRdigestdplyrellipseevaluatefansifarverfastmapfilelockfontawesomeforeignFormulafsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegplotsgraphgridExtraGSEABasegtablegtoolsHeatplushgu133a.dbhighrHmischmshopachhtmlTablehtmltoolshtmlwidgetshttrhttr2inlineIRangesisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglatticeleapslifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellmvtnormnlmennetopensslorg.Hs.eg.dbpcaPPpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsRBGLRColorBrewerrlangrmarkdownrobustbaserpartrrcovRSQLiterstudioapiS4VectorssassscalesstatmodstringistringrsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisviridisLitewithrxfunXMLxml2xtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Test correlation between gene expression and phenotype. | phenoTest-package phenoTest |
| Summary plots for gene signature vs phenotype association | barplotSignatures barplotSignifSignatures |
| Methods for Function barplotSignatures in Package `phenoTest' | barplotSignatures,epheno,character-method barplotSignatures,epheno,GeneSet-method barplotSignatures,epheno,GeneSetCollection-method barplotSignatures,epheno,list-method barplotSignatures-methods |
| Methods for Function barplotSignifSignatures in Package `phenoTest' | barplotSignifSignatures,epheno,character-method barplotSignifSignatures,epheno,GeneSet-method barplotSignifSignatures,epheno,GeneSetCollection-method barplotSignifSignatures,epheno,list-method barplotSignifSignatures-methods |
| Test association of clusters with phenotype. | ClusterPhenoTest |
| epheno object. | epheno |
| Class "epheno" | approach,epheno-method dim,epheno-method epheno-class getFc,epheno-method getHr,epheno-method getMeans,epheno-method getPostProbs,epheno-method getPvals,epheno-method getSignif,epheno-method getSummaryDif,epheno-method logFcHr,epheno-method p.adjust.method,epheno-method phenoClass,epheno-method phenoNames,epheno-method show,epheno-method [,epheno,ANY,ANY-method |
| Create html files and plots from an epheno object. | epheno2html |
| Example data. | eset |
| Example data. | eset.genelevel |
| Filter ExpressionSet to keep one probeset per gene. | eset2genelevel |
| Export object to comma-separated text file. | export2CSV |
| Methods for Function export2CSV in Package 'phenoTest' | export2CSV,epheno-method export2CSV-methods |
| Tests univariate association between a list of phenotype variables and gene expression. | ExpressionPhenoTest |
| Find copy number regions using expression data in a similar way ACE does. | findCopyNumber |
| Find genes that are in given areas. | genesInArea |
| Substract element's of a gseaSignaturesSign or gseaSignaturesVar object (obtained using the gseaSignatures function). | getEs getEsSim getFcHr getNes |
| Obtain chromosome positions for each gene. | getEsPositions |
| Getters for the epheno object: | approach getFc getHr getMeans getPostProbs getPvals getSignif getSummaryDif logFcHr p.adjust.method phenoClass phenoNames [,epheno,ANY,ANY,ANY-method |
| Get phenotypic variables that were tested. | getVars2test |
| Methods for Function getVars2test in Package `phenoTest' | getVars2test,epheno-method getVars2test-methods |
| GSEA (Gene Set Enrichment Analysis). | gsea |
| Subset an object of class gseaData. | gsea.selGsets gsea.selVars |
| Export an object of class gseaData to an html file. | gsea2html |
| Class "gseaData" | getEs,gseaData-method getEsSim,gseaData-method getFcHr,gseaData-method gseaData-class show,gseaData-method |
| Compute ES (enrichment scores) and es.sim (simulated enrichment scores) for given phenotipic variable(s) and signature(s). | gseaSignatures |
| Class "gseaSignatures" ES and EsSim container. | gseaSignatures-class |
| Methods for Function gseaSignatures in Package `phenoTest' | gseaSignatures,ANY,character-method gseaSignatures,ANY,GeneSet-method gseaSignatures,epheno,GeneSetCollection-method gseaSignatures,epheno,list-method gseaSignatures,matrix,GeneSetCollection-method gseaSignatures,matrix,list-method gseaSignatures,numeric,GeneSetCollection-method gseaSignatures,numeric,list-method gseaSignatures-methods |
| Class "gseaSignaturesSign" | getEs,gseaSignaturesSign-method getEsSim,gseaSignaturesSign-method getFcHr,gseaSignaturesSign-method gseaSignaturesSign-class gseaSignificance,gseaSignaturesSign-method |
| Class "gseaSignaturesVar" | getEs,gseaSignaturesVar-method getEsSim,gseaSignaturesVar-method getFcHr,gseaSignaturesVar-method gseaSignaturesVar-class gseaSignificance,gseaSignaturesVar-method |
| ES' (enrichment scores) sifgnificance. | gseaSignificance |
| Class "gseaSignificanceSign" | gseaSignificanceSign-class |
| Class "gseaSignificanceVar" | gseaSignificanceVar-class |
| Produce heatmap from phenotype data. | heatmapPhenoTest |
| Methods for Function heatmapPhenoTest in Package `phenoTest' | heatmapPhenoTest,ExpressionSet,character-method heatmapPhenoTest,ExpressionSet,GeneSet-method heatmapPhenoTest,ExpressionSet,GeneSetCollection-method heatmapPhenoTest,ExpressionSet,list-method heatmapPhenoTest,ExpressionSet,missing-method heatmapPhenoTest-methods |
| Adjust p values of an epheno object. | pAdjust |
| Methods for Function pAdjust in Package `phenoTest' | pAdjust,epheno-method pAdjust-methods |
| Principal components plot. | pca |
| GSEA-like Plot. | plot.gseaData |
| GSEA-like Plot. | plot.gseaSignaturesSign plot.gseaSignaturesVar |
| Methods for Function show in Package `methods'. | show,AnnotatedDataFrame-method show,ANY-method show,classRepresentation-method show,container-method show,eSet-method show,genericFunction-method show,gseaSignaturesSign-method show,gseaSignaturesVar-method show,gseaSignificanceSign-method show,gseaSignificanceVar-method show,LargeDataObject-method show,MethodDefinition-method show,MethodSelectionReport-method show,MethodWithNext-method show,MIAME-method show,namedList-method show,ObjectsWithPackage-method show,oldClass-method show,ScalarCharacter-method show,ScalarObject-method show,signature-method show,TestResults-method show,traceable-method show,Versioned-method show,Versions-method show,VersionsNull-method show-methods |
| Plots the Cox proportional hazard smoothed by gene expression level. | smoothCoxph |
| Obtain a data.frame with the pvalues and fdr for all signatures and variables of a gseaData object. | summary.gseaData |
| Obtain a data.frame with the pvalues and fdr for all signatures and variables of a gseaSignificanceSign or gseaSignificanceVar object. | summary.gseaSignificanceSign summary.gseaSignificanceVar |
| Write a data.frame to an html file. | write.html |
