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