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"object": "epheno", "file": "epheno.RData", "class": [ "epheno" ], "fields": [], "table": false, "tojson": false }, { "name": "eset", "title": "Example data.", "object": "eset", "file": "eset.genelevel.RData", "class": [ "ExpressionSet" ], "fields": [], "table": false, "tojson": false }, { "name": "eset.genelevel", "title": "Example data.", "object": "eset.genelevel", "file": "eset.genelevel.RData", "class": [ "ExpressionSet" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "phenoTest-package", "title": "Test correlation between gene expression and phenotype.", "topics": [ "phenoTest-package", "phenoTest" ] }, { "page": "plots4epheno", "title": "Summary plots for gene signature vs phenotype association", "topics": [ "barplotSignatures", "barplotSignifSignatures" ] }, { "page": "barplotSignatures-methods", "title": "Methods for Function barplotSignatures in Package `phenoTest'", "topics": [ "barplotSignatures,epheno,character-method", "barplotSignatures,epheno,GeneSet-method", "barplotSignatures,epheno,GeneSetCollection-method", "barplotSignatures,epheno,list-method", "barplotSignatures-methods" ] }, { "page": "barplotSignifSignatures-methods", "title": "Methods for Function barplotSignifSignatures in Package `phenoTest'", "topics": [ "barplotSignifSignatures,epheno,character-method", "barplotSignifSignatures,epheno,GeneSet-method", "barplotSignifSignatures,epheno,GeneSetCollection-method", "barplotSignifSignatures,epheno,list-method", "barplotSignifSignatures-methods" ] }, { "page": "ClusterPhenoTest", "title": "Test association of clusters with phenotype.", "topics": [ "ClusterPhenoTest" ] }, { "page": "epheno", "title": "epheno object.", "topics": [ "epheno" ] }, { "page": "epheno-class", "title": "Class \"epheno\"", "topics": [ "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" ] }, { "page": "epheno2html", "title": "Create html files and plots from an epheno object.", "topics": [ "epheno2html" ] }, { "page": "eset", "title": "Example data.", "topics": [ "eset" ] }, { "page": "eset.genelevel", "title": "Example data.", "topics": [ "eset.genelevel" ] }, { "page": "eset2genelevel", "title": "Filter ExpressionSet to keep one probeset per gene.", "topics": [ "eset2genelevel" ] }, { "page": "export2CSV", "title": "Export object to comma-separated text file.", "topics": [ "export2CSV" ] }, { "page": "export2CSV-methods", "title": "Methods for Function export2CSV in Package 'phenoTest'", "topics": [ "export2CSV,epheno-method", "export2CSV-methods" ] }, { "page": "ExpressionPhenoTest", "title": "Tests univariate association between a list of phenotype variables and gene expression.", "topics": [ "ExpressionPhenoTest" ] }, { "page": "findCopyNumber", "title": "Find copy number regions using expression data in a similar way ACE does.", "topics": [ "findCopyNumber" ] }, { "page": "genesInArea", "title": "Find genes that are in given areas.", "topics": [ "genesInArea" ] }, { "page": "getGseaSignatures", "title": "Substract element's of a gseaSignaturesSign or gseaSignaturesVar object (obtained using the gseaSignatures function).", "topics": [ "getEs", "getEsSim", "getFcHr", "getNes" ] }, { "page": "getEsPositions", "title": "Obtain chromosome positions for each gene.", "topics": [ "getEsPositions" ] }, { "page": "ephenoGetters", "title": "Getters for the epheno object:", "topics": [ "approach", "getFc", "getHr", "getMeans", "getPostProbs", "getPvals", "getSignif", "getSummaryDif", "logFcHr", "p.adjust.method", "phenoClass", "phenoNames", "[,epheno,ANY,ANY,ANY-method" ] }, { "page": "getVars2test", "title": "Get phenotypic variables that were tested.", "topics": [ "getVars2test" ] }, { "page": "getVars2test-methods", "title": "Methods for Function getVars2test in Package `phenoTest'", "topics": [ "getVars2test,epheno-method", "getVars2test-methods" ] }, { "page": "gsea", "title": "GSEA (Gene Set Enrichment Analysis).", "topics": [ "gsea" ] }, { "page": "gsea.subset", "title": "Subset an object of class gseaData.", "topics": [ "gsea.selGsets", "gsea.selVars" ] }, { "page": "gsea2html", "title": "Export an object of class gseaData to an html file.", "topics": [ "gsea2html" ] }, { "page": "gseaData-class", "title": "Class \"gseaData\"", "topics": [ "getEs,gseaData-method", "getEsSim,gseaData-method", "getFcHr,gseaData-method", "gseaData-class", "show,gseaData-method" ] }, { "page": "gseaSignatures", "title": "Compute ES (enrichment scores) and es.sim (simulated enrichment scores) for given phenotipic variable(s) and signature(s).", "topics": [ "gseaSignatures" ] }, { "page": "gseaSignatures-class", "title": "Class \"gseaSignatures\" ES and EsSim container.", "topics": [ "gseaSignatures-class" ] }, { "page": "gseaSignatures-methods", "title": "Methods for Function gseaSignatures in Package `phenoTest'", "topics": [ "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" ] }, { "page": "gseaSignaturesSign-class", "title": "Class \"gseaSignaturesSign\"", "topics": [ "getEs,gseaSignaturesSign-method", "getEsSim,gseaSignaturesSign-method", "getFcHr,gseaSignaturesSign-method", "gseaSignaturesSign-class", "gseaSignificance,gseaSignaturesSign-method" ] }, { "page": "gseaSignaturesVar-class", "title": "Class \"gseaSignaturesVar\"", "topics": [ "getEs,gseaSignaturesVar-method", "getEsSim,gseaSignaturesVar-method", "getFcHr,gseaSignaturesVar-method", "gseaSignaturesVar-class", "gseaSignificance,gseaSignaturesVar-method" ] }, { "page": "gseaSignificance", "title": "ES' (enrichment scores) sifgnificance.", "topics": [ "gseaSignificance" ] }, { "page": "gseaSignificanceSign-class", "title": "Class \"gseaSignificanceSign\"", "topics": [ "gseaSignificanceSign-class" ] }, { "page": "gseaSignificanceVar-class", "title": "Class \"gseaSignificanceVar\"", "topics": [ "gseaSignificanceVar-class" ] }, { "page": "heatmapPhenoTest", "title": "Produce heatmap from phenotype data.", "topics": [ "heatmapPhenoTest" ] }, { "page": "heatmapPhenoTest-methods", "title": "Methods for Function heatmapPhenoTest in Package `phenoTest'", "topics": [ "heatmapPhenoTest,ExpressionSet,character-method", "heatmapPhenoTest,ExpressionSet,GeneSet-method", "heatmapPhenoTest,ExpressionSet,GeneSetCollection-method", "heatmapPhenoTest,ExpressionSet,list-method", "heatmapPhenoTest,ExpressionSet,missing-method", "heatmapPhenoTest-methods" ] }, { "page": "pAdjust", "title": "Adjust p values of an epheno object.", "topics": [ "pAdjust" ] }, { "page": "pAdjust-methods", "title": "Methods for Function pAdjust in Package `phenoTest'", "topics": [ "pAdjust,epheno-method", "pAdjust-methods" ] }, { "page": "pca", "title": "Principal components plot.", "topics": [ "pca" ] }, { "page": "plot.gsea", "title": "GSEA-like Plot.", "topics": [ "plot.gseaData" ] }, { "page": "plot.gseaSignatures", "title": "GSEA-like Plot.", "topics": [ "plot.gseaSignaturesSign", "plot.gseaSignaturesVar" ] }, { "page": "show-methods", "title": "Methods for Function show in Package `methods'.", "topics": [ "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", 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