ELMER                   ELMER (Enhancer Linking by
                        Methylation/Expression Relationships)
Get.Pvalue.p            Calculate empirical Pvalue
GetNearGenes            GetNearGenes to collect nearby genes for one
                        locus.
Stat.diff.meth          Stat.diff.meth
Stat.nonpara            U test (non parameter test) for permutation.
                        This is one probe vs nearby gene which is good
                        for computing each probes for nearby genes.
Stat.nonpara.permu      Stat.nonpara.permu
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.
TFsurvival.plot         Creates survival plot of based on the
                        expression of a TF
addDistNearestTSS       Calculate the distance between probe and gene
                        TSS
addMutCol               Adds mutation information to MAE
calcDistNearestTSS      Calculate distance from region to nearest TSS
calculateEnrichement    Calculate motif Erichment
createBigWigDNAmetArray
                        Create a bigwig file for IGV visualization of
                        DNA methylation data (Array)
createIGVtrack          Create a junction track for IGV visualization
                        of interection
createMAE               Construct a Multi Assay Experiment for ELMER
                        analysis
createMotifRelevantTfs
                        Get family of transcription factors
createSummaryDocument   Create summary document for TCGA.pipe function
createTSVTemplates      Create examples files for Sample mapping and
                        information used in createMAE function
findMotifRegion         Use Hocomoco motif and homer to identify motifs
                        in a given region
get.TFs                 get.TFs to identify regulatory TFs.
get.diff.meth           Identify hypo/hyper-methylated CpG sites
                        between two groups (i.e. normal vs tumor
                        samples, treated vs untreated).
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.
get.tab                 summarize MR TF as a binary table with 1 if TF
                        was found in the analysis, 0 if not
get.tabs                Creating matrix for MR TF heatmap
get450K                 get450K to download HM40K DNA methylation data
                        for certain cancer types from TCGA website.
                        @description get450K is a function to download
                        latest version of HM450K DNA methylation for
                        all samples of certain cancer types from GDC
                        website.
getClinic               getClinic to download clinic data for certain
                        cancer types from TCGA website.
getExp                  Get Gene expression object from MAE
getExpSamples           Get Gene expression object samples from MAE
getGeneID               getGeneID to report gene id from symbol
getMet                  Get DNA methylation object from MAE
getMetSamples           Get DNA methylation object samples from MAE
getRNAseq               getRNAseq to download all RNAseq data for a
                        certain cancer type from TCGA.
getRandomPairs          Get random pairs
getRegionNearGenes      Identifies nearest genes to a region
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.
getTF                   Get human TF list from the UNiprot database
getTFBindingSites       Get MR TF binding regions infered by ELMER
getTFtargets            Get TF target genes
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.
heatmapGene             Heatmap for correlation between probes DNA
                        methylation and a single gene expression.
heatmapPairs            Heatmap of pairs gene and probes
                        anti-correlated
lm_eqn                  lable linear regression formula
metBoxPlot              scatter.plot to plot scatter plots between gene
                        expression and DNA methylation.
motif.enrichment.plot   motif.enrichment.plot to plot bar plots showing
                        motif enrichment ORs and 95% confidence
                        interval for ORs
preAssociationProbeFiltering
                        Filtering probes
promoterMeth            promoterMeth to calculate associations of gene
                        expression with DNA methylation at promoter
                        regions
render_report           Build report for TCGA.pipe function
scatter                 scatter
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.
summarizeTF             Make MR TF binary table
