about                   about canceR
canceR                  main function
canceR_Issue            canceR Report Issue
canceR_Vignette         open pdf vignette
cbind.na                bind non equal colunm
CGDS                    CGDS connect object to cBioPortal
dialogGeneClassifier    Dialogue Box for gene classifier setting:
                        sample size and postprob threshold
dialoggetGeneListMSigDB
                        Multi-select choice of gene sets from loaded
                        MSigDB
dialogMetOption         Dialog Box to set methylation options
dialogMut               Dialog bos to set returned Mutation information
dialogOptionCircos      Checkbox to select dimensions
dialogOptionGSEAlm      Dialogbox to select variables from Clinical
                        data
dialogOptionPhenoTest   Checkbox to select variables from clinical data
dialogPlotOption_SkinCor
                        Checkbox to select variables for plotting
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 to Specify Mutation using Regular
                        Expression. Search specific mutation using
                        regular expression.
dialogSummary_GSEA      Dialog Box to specify phenotype (variable) used
                        in last GSEA-R to get Summary Results. This
                        function ask the user to specify the phenotype
                        (variable).
displayInTable          Display matrix in tcltk table
getCases                Get cases for selected Studies. The Cases are
                        the descrption of the samples from patients.
                        The samples can be subdivided by the type of
                        assays as, sequencing, CNA, Mutation,
                        Methylation.
getCasesGenProfs        get Cases and Genetic Profiles of selected
                        Studies.
getCircos               get Circos Layout for selected studies and
                        selected dimensions
getClinicalDataMatrix   get matrix with clinical from file
getClinicData_MultipleCases
                        get Clinical Data for Multiple Cases. User
                        needs to select at least one case to run this
                        function. Get clinical data for more one or
                        multiple cases.
getCor_ExpCNAMet        Get gene correlation for multiple dimensions.
geteSet                 Built Expression Set (eSet) from profile data.
getFreqMutData          get mutation frequency
getGCT_CLSfiles         get Profile (GCT file) and Phenotype (CLS file)
                        Data from Disease.
getGCTCLSExample        get GCT and CLS example files.
getGeneExpMatrix        get matrix with gene expression from file
getGeneList             User needs to specify which gene is interesting
                        to get genomic cancer data. The gene must be
                        with Symbol and one gene by line.
getGeneListExample      get Gene List from examples. User can select
                        one from available gene list
getGeneListFromMSigDB   get gene list from MSigDB
getGenesClassifier      get Genes Classifier
getGenesTree_MultipleCases
                        Get successively trees of genes list for
                        multiple cases
getGenesTree_SingleCase
                        classify genes in tree for two phenotypes in
                        the same case(disease).
getGenProfs             Get Genetic Profile from selected Studies
getGSEAlm_Diseases      get GSEA linear modeling by studies (diseases)
getGSEAlm_Variables     get GSEA linear modeling by variables
                        (phenotype)
getInTable              get dataframe in TK/TCL table
getListProfData         Get list of data frame with profiles data
                        (CNA,mRNA, Methylation, Mutation...)
getMegaProfData         Get profile data for more than 500 genes list.
getMetDataMultipleGenes
                        get Methylation data for multiple genes
getMSigDB               Reduce MSigDB size for only gene list
getMSigDBExample        get example of .gmt file from MSigDB (Broad
                        Institute)
getMSigDBfile           Dialog Box to Select MSigDB Files from drive
getMutData              get Mutation data for multiple genes
getPhenoTest            Associate phenotype to Studies (cancers)
getProfData             Search and get genetic profiles (CNA,mRNA,
                        Methylation, Mutation...)
getProfilesDataMultipleGenes
                        get Profles Data of multiple genes
getProfilesDataSingleGene
                        get Profiles Data for a Single Gene.
getSpecificMut          get specific Mutation data for multiple genes
getSummaryGSEA          get Summary results from GSEA-R (Broad
                        Institute)
getSurvival             Survival plot
getTextWin              get text in tcltk windows
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
Match_GeneList_MSigDB   Search MSigDb that overlap gene list
modalDialog             Dialog box to specify Gene Symbol.
myGlobalEnv             myGlobalEnv
OLD.GSEA.EnrichmentScore
                        OLD.GSEA.EnrichmentScore
plot_1Gene_2GenProfs    Plotting two genetic profiles for one Gene
plot_2Genes_1GenProf    plot correlation of two genes expressions.
plotModel               model plotting with tcltk
rbind.na                bind non equal row
Run.GSEA                The main function to run GSEA-R from Broad
                        Institute
setWorkspace            Setting work Directory and output folders.At
                        starting window, user needs to set work
                        directory for output data. The function is foud
                        in File menu.
test.CGDS               S3 method to test cBioPortal connection
testCheckedCaseGenProf
                        Testing checked appropriate Cases for
                        appropriate Genetic profiles.
UnifyRowNames           Unify row names in data frame with the same
                        order of gene list.
