Example data.
Create html files and plots from an epheno object.
Example data.
barplotSignifSignatures-methods
Methods for Function barplotSignifSignatures in Package `phenoTest'
barplotSignatures-methods
Methods for Function barplotSignatures in Package `phenoTest'
getters for the epheno object
Getters for the epheno object:
epheno object.
Test association of clusters with phenotype.
Class "epheno"
Filter ExpressionSet to keep one probeset per gene.
Export object to comma-separated text file.
Methods for Function export2CSV in Package 'phenoTest'
Tests univariate association between a list of phenotype
variables and gene expression.
Create a list of gene sets based on KEGG pathways terms.
Methods for Function getVars2test in Package `phenoTest'
Obtain chromosome positions for each gene.
Create a list of gene sets based on GO pathways terms.
get gseaSignatures' elements
Substract element's of a gseaSignaturesSign or gseaSignaturesVar object (obtained using the
gseaSignatures function).
Find copy number regions using expression data in a similar way ACE does.
Find genes that are in given areas.
Compute ES (enrichment scores) and es.sim (simulated enrichment scores)
for given phenotipic variable(s) and signature(s).
Plots the Cox proportional hazard smoothed by gene expression level.
Class "gseaSignaturesSign"
gseaSignificanceVar-class
Class "gseaSignificanceVar"
gseaSignificanceSign-class
Class "gseaSignificanceSign"
Class "gseaSignatures" ES and EsSim container.
Obtain a data.frame with the pvalues and fdr for all signatures and
variables of a gseaData object.
Methods for Function gseaSignatures in Package `phenoTest'
Class "gseaSignaturesVar"
ES' (enrichment scores) sifgnificance.
Methods for Function show in Package `methods'.
Perform Gene Set Enrichment Analysis (GSEA) of Gene Ontologies (GO) and
Kegg gene sets.
Methods for Function pAdjust in Package `phenoTest'
Subset an object of class gseaData.
Adjust p values of an epheno object.
Summary plots for gene signature vs phenotype association
Class "gseaData"
Export an object of class gseaData to an html file.
Principal components plot.
Test correlation between gene expression and phenotype.
Get phenotypic variables that were tested.
GSEA (Gene Set Enrichment Analysis).
Obtain a data.frame with the pvalues and fdr for all signatures and
variables of a gseaSignificanceSign or gseaSignificanceVar object.
Produce heatmap from phenotype data.
Write a data.frame to an html file.
GSEA-like Plot.
Methods for Function heatmapPhenoTest in Package `phenoTest'
GSEA-like Plot.