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