ClinicalData            ClinicalData
GSEA                    GSEA-R (Broad Institute)
GSEA.Analyze.Sets       GSEA.Analyze.Sets
GSEA.ConsPlot           GSEA.ConsPlot
GSEA.EnrichmentScore    GSEA.EnrichmentScore
GSEA.EnrichmentScore2   GSEA.EnrichmentScore2
GSEA.Gct2Frame          GSEA.Gct2Frame
GSEA.Gct2Frame2         GSEA.Gct2Frame2
GSEA.GeneRanking        GSEA.GeneRanking
GSEA.HeatMapPlot        GSEA.HeatMapPlot
GSEA.HeatMapPlot2       GSEA.HeatMapPlot2
GSEA.NormalizeCols      GSEA.NormalizeCols
GSEA.NormalizeRows      GSEA.NormalizeRows
GSEA.ReadClsFile        GSEA.ReadClsFile
GSEA.Res2Frame          GSEA.Res2Frame
GSEA.Threshold          GSEA.Threshold
GSEA.VarFilter          GSEA.VarFilter
GSEA.write.gct          GSEA.write.gct
GeneExpMatrix           Profile data
Match_GeneList_MSigDB   Match_GeneList_MSigDB
OLD.GSEA.EnrichmentScore
                        OLD.GSEA.EnrichmentScore
Run.GSEA                The main function to run GSEA-R from Broad
                        Institute
about                   get brief information and help.
canceR                  Main function of canceR package.
canceRHelp              canceRHelp
canceR_Vignette         Get Vignette
cbind.na                cbind.na
dialogGeneClassifier    dialogGeneClassifier
dialogMetOption         dialog box to specify Methylation rate
                        threshold of silencing genes.
dialogMut               dialog box to specify Animo Acid changes using
                        regular expression
dialogOptionGSEAlm      Dialog Box Option for GSEAlm
dialogOptionPhenoTest   Dialog Box to specify Variables for PhenoTest
                        function.
dialogPlotOption_SkinCor
                        dialogPlotOption_SkinCor
dialogSamplingGSEA      Dialog Box for Sampling patients from
                        expression profile data used for GSEA-R (Broad
                        Institute)
dialogSelectFiles_GSEA
                        Dialog Box to Select GCT, CLS, GMT and output
                        Files for GSEA-R (Broad Institute)
dialogSpecificMut       dialog box tp Specify Mutation using Regular
                        Expression.
dialogSummary_GSEA      Dialog Box to specify phenotype (variable) used
                        in last GSEA-R to get Summary Results.
displayInTable          Display In Table
getCases                Get cases for selected Studies
getCasesGenProfs        get Cases and Genetic Profiles of selected
                        Studies.
getClinicData_MultipleCases
                        get Clinical Data for Multiple Cases
getClinicalDataMatrix   getClinicalDataMatrix
getGCTCLSExample        getGCTCLSExample
getGCT_CLSfiles         get Profile (GCT file) and Phenotype (CLS file)
                        Data from Disease.
getGSEAlm_Diseases      Get Gene Set Enrichment Analysis linear
                        modeling for two Diseases.
getGSEAlm_Variables     Get Gene Set Enrichment Analysis linear
                        modeling for two phenotypes (variables) in the
                        same disease.
getGenProfs             Get Genetic Profile from selected Studies
getGeneExpMatrix        load matrix from file
getGeneList             get Gene List from file.
getGeneListExample      get Gene List from examples
getGenesClassifier      Ranking Genes by Diseases.
getGenesTree_MultipleCases
                        getGenesTree_MultipleCases
getGenesTree_SingleCase
                        getGenesTree_SingleCase
getInTable              getInTable
getMSigDB               getMSigDB
getMSigDBExample        getMSigDBExample
getMSigDBfile           getMSigDBfile
getMegaProfData         getMegaProfData
getMetDataMultipleGenes
                        get Methylation Data for Multiple Genes.
getMutData              get Mutation Data for gene list.
getPhenoTest            Associate Phenotypes (variables) from Clinical
                        data to gene expression profile.
getProfilesDataMultipleGenes
                        get Profiles Data of Multiple Genes.
getProfilesDataSingleGene
                        get Profiles Data for a Single Gene.
getSpecificMut          get Specific Mutation using Amino Acid changes.
getSummaryGSEA          get Summary results from GSEA-R (Broad
                        Institute)
getTextWin              getTextWin
geteSet                 Build expression Set (Biobase)
modalDialog             Dialog box to specify Gene Symbol.
myGlobalEnv             myGlobalEnv
plotModel               plot Model
plot_1Gene_2GenProfs    Plotting two genetic profiles for one Gene
plot_2Genes_1GenProf    plot correlation of two genes expressions.
rbind.na                rbind.na
setWorkspace            Setting work Directory and output folders.
testCheckedCaseGenProf
                        Testing checked appropriate Cases for
                        appropriate Genetic profiles.
