ELMER                   ELMER is designed to use DNA methylation and
                        gene expression from a large number of samples
                        to infere regulatory element landscape and
                        transcription factor network in primary tissue.
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
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
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.
                        @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.
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
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.
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
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.
