GetNearGenes            GetNearGenes to collect nearby genes for one
                        locus.
MEE.data-class          MEE.data An S4 class contains 5 slots:
                        methylation, expression, sample information,
                        probe information and gene information.
                        MEE.data class are the main input for main
                        functions.
Pair-class              An S4 class that pairs information, probe
                        information and gene information.
TCGA.pipe               ELMER analysis pipeline for TCGA data.
TF.rank.plot            TF.rank.plot to plot the scores (-log10(P
                        value)) which assess the correlation between TF
                        expression and average DNA methylation at motif
                        sites.
fetch.mee               fetch.mee to generate MEE.data class object.
fetch.pair              fetch.pair to generate Pair class object.
get.TFs                 get.TFs to identify regulatory TFs.
get.diff.meth           get.diff.meth to identify hypo/hyper-methylated
                        CpG sites on HM450K between control and
                        experimental groups such as normal verus tumor
                        samples.
get.enriched.motif      get.enriched.motif to identify the
                        overrepresented motifs in a set of probes
                        (HM450K) regions.
get.feature.probe       get.feature.probe to select probes within
                        promoter regions or distal regions.
get.pair                get.pair to predict enhancer-gene linkages.
get.permu               get.permu to generate permutation results for
                        calculation of empirical P values for each
                        enhancer-gene linkage.
get450K                 get450K to download HM40K DNA methylation data
                        for certain cancer types from TCGA website.
getClinic               getClinic to download clinic data for certain
                        cancer types from TCGA website.
getExp                  getExp to extract RNA expression slot from a
                        MEE.data class object.
getGeneID               getGeneID to report gene id from symbol
getGeneInfo             getGeneInfo to extract geneInfo slot from
                        MEE.data or Pair object.
getMeth                 getMeth to extract DNA methylation slot from a
                        MEE.data class object.
getPair                 getPair to extract pairInfo slot from Pair
                        object.
getProbeInfo            getProbeInfo to extract probeInfo slot from
                        MEE.data or Pair object.
getRNAseq               getRNAseq to download all RNAseq data for a
                        certain cancer type from TCGA.
getSample               getSample to extract sample information from
                        MEE.data object.
getSymbol               getSymbol to report gene symbol from id
getTCGA                 getTCGA to download DNA methylation, RNA
                        expression and clinic data for all samples of
                        certain cancer type from TCGA.
motif.enrichment.plot   motif.enrichment.plot to plot bar plots showing
                        motif enrichment ORs and 95% confidence
                        interval for ORs
promoterMeth            promoterMeth to calculate associations of gene
                        expression with DNA methylation at promoter
                        regions.
scatter.plot            scatter.plot to plot scatter plots between gene
                        expression and DNA methylation.
schematic.plot          schematic.plot to plot schematic plots showing
                        the locations of genes and probes.
txs                     txs to fetch USCS gene annotation (transcripts
                        level) from Bioconductor package Homo.sapians.
                        If upstream and downstream are specified in TSS
                        list, promoter regions of USCS gene will be
                        generated.
