.extractPriMiRNA        The extractPriMiRNA function
addDistNearestTSS       Calculate the distance between probe and gene
                        TSS
addGeneNames            The addGeneNames function
calcDistNearestTSS      Calculate distance from region to nearest TSS
ClusterProbes           The ClusterProbes function
EpiMix                  The EpiMix function
EpiMix_getInfiniumAnnotation
                        The EpiMix_getInfiniumAnnotation function
EpiMix_PlotGene         The EpiMix_PlotGene function
EpiMix_PlotModel        The EpiMix_PlotModel function.
EpiMix_PlotProbe        The EpiMix_PlotProbe function
EpiMix_PlotSurvival     EpiMix_PlotSurvival function
filterProbes            The filterProbes function
find_miRNA_targets      The find_miRNA_targets function
functionEnrich          The functionEnrich function
generateFunctionalPairs
                        The generateFunctionalPairs function
GEO_Download_DNAMethylation
                        The GEO_Download_DNAmethylation function
GEO_Download_GeneExpression
                        The GEO_Download_GeneExpression function
GEO_GetSampleInfo       The GEO_GetSampleInfo function
GEO_getSampleMap        the GEO_getSampleMap function
Get.Pvalue.p            Calculate empirical Pvalue
getFeatureProbe         getFeatureProbe to select probes within
                        promoter regions or distal regions.
getMethStates_Helper    The getMethStates_Helper function
GetNearGenes            GetNearGenes to collect nearby genes for one
                        locus.
getProbeAnnotation      The getProbeAnnotation function
getRegionNearGenes      Identifies nearest genes to a region
GetSurvivalProbe        The GetSurvivalProbe function
getTSS                  getTSS to fetch GENCODE gene annotation
                        (transcripts level) from Bioconductor package
                        biomaRt If upstream and downstream are
                        specified in TSS list, promoter regions of
                        GENCODE gene will be generated.
MethylMix_Predict       The MethylMix_Predict function
predictOneGene          The predictOneGene function
Preprocess_DNAMethylation
                        The Preprocess_DNAMethylation function
Preprocess_GeneExpression
                        The Preprocess_GeneExpression function
removeDuplicatedGenes   The removeDuplicatedGenes function
TCGA_Download_DNAmethylation
                        The TCGA_Download_DNAmethylation function
TCGA_Download_GeneExpression
                        The TCGA_Download_GeneExpression function
TCGA_GetData            The TCGA_GetData function
TCGA_GetSampleInfo      The TCGA_GetSampleInfo function
TCGA_Preprocess_DNAmethylation
                        The TCGA_Preprocess_DNAmethylation function
TCGA_Preprocess_GeneExpression
                        The TCGA_Preprocess_GeneExpression function
TCGA_Select_Dataset     The TCGA_Select_Dataset function
translateMethylMixResults
                        The translateMethylMixResults function
validEpigenomes         The validEpigenomes function
