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