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: |