TCGADownloader          Download TCGA gene expression, DNA methylation,
                        and clinical datasets and compile them into a
                        MultiAssayExperiment object
TENETCacheAllData       Cache all online datasets required by TENET
                        examples and optional features
easyTENET               Run the step 1 through step 6 functions with
                        default arguments
humanTranscriptionFactorList
                        Human transcription factor list
step1MakeExternalDatasets
                        Create a GRanges object representing putative
                        regulatory element regions, based on the data
                        sources selected for inclusion, to be used in
                        later TENET steps
step2GetDifferentiallyMethylatedSites
                        Identify differentially methylated RE DNA
                        methylation sites
step3GetAnalysisZScores
                        Calculate Z-scores comparing the mean
                        expression of each gene in the case samples
                        that are hyper- or hypomethylated for each RE
                        DNA methylation site chosen in step 2
step4SelectMostSignificantLinksPerDNAMethylationSite
                        Select the most significant RE DNA methylation
                        site-gene links to each RE DNA methylation site
step5OptimizeLinks      Find final RE DNA methylation site-gene links
                        using various optimization metrics
step6DNAMethylationSitesPerGeneTabulation
                        Tabulate the total number of RE DNA methylation
                        sites linked to each of the genes
step7ExpressionVsDNAMethylationScatterplots
                        Create scatterplots displaying the expression
                        of the top genes and the methylation levels of
                        each of their linked RE DNA methylation sites,
                        along with copy number variation, somatic
                        mutation, and purity data, if provided by the
                        user
step7LinkedDNAMethylationSiteCountHistograms
                        Create histograms displaying the number of
                        genes or transcription factors linked to a
                        given number of RE DNA methylation sites
step7LinkedDNAMethylationSitesMotifSearching
                        Perform motif searching for transcription
                        factor motifs in the vicinity of RE DNA
                        methylation sites linked to the specified
                        transcription factors
step7SelectedDNAMethylationSitesCaseVsControlBoxplots
                        Generate boxplots comparing the methylation
                        level of the specified RE DNA methylation sites
                        in case and control samples
step7StatesForLinks     Identify which of the case samples harbor each
                        of the identified regulatory element DNA
                        methylation site-gene links
step7TopGenesCaseVsControlExpressionBoxplots
                        Create boxplots comparing the expression level
                        of the top genes/transcription factors in case
                        and control samples
step7TopGenesCircosPlots
                        Generate Circos plots displaying the links
                        between top identified genes and each of the RE
                        DNA methylation sites linked to them
step7TopGenesDNAMethylationHeatmaps
                        Generate heatmaps displaying the methylation
                        level of all RE DNA methylation sites linked to
                        the top genes/transcription factors, along with
                        the expression of those genes in the column
                        headers, in the case samples within the
                        supplied MultiAssayExperiment object
step7TopGenesExpressionCorrelationHeatmaps
                        Generate mirrored heatmaps displaying the
                        correlation of the expression values of the top
                        genes/TFs
step7TopGenesOverlappingLinkedDNAMethylationSitesHeatmaps
                        Generate binary heatmaps displaying which of
                        the top genes/transcription factors share links
                        with each of the unique regulatory element DNA
                        methylation sites linked to at least one top
                        gene/TF
step7TopGenesSurvival   Perform Kaplan-Meier and Cox regression
                        analyses to assess the association of top gene
                        expression and linked RE DNA methylation site
                        methylation with patient survival
step7TopGenesTADTables
                        Create tables using user-supplied topologically
                        associating domain (TAD) information which
                        identify the topologically associating domains
                        containing each RE DNA methylation site linked
                        to the top genes/transcription factors, as well
                        as other genes in the same topologically
                        associating domain as potential downstream
                        targets
step7TopGenesUCSCBedFiles
                        Create bed-formatted interact files which can
                        be loaded on the UCSC Genome Browser to display
                        links between top genes and transcription
                        factors and their linked RE DNA methylation
                        sites
step7TopGenesUserPeakOverlap
                        Identify if RE DNA methylation sites linked to
                        top genes/transcription factors are located
                        within a specific distance of specified genomic
                        regions
