MethReg                 MethReg: functional annotation of DMRs
                        identified in epigenome-wide association
                        studies
clinical                TCGA-COAD clinical matrix for 38 samples
                        retrieved from GDC using TCGAbiolinks
cor_dnam_target_gene    Evaluate correlation of DNA methylation region
                        and target gene expression
cor_tf_target_gene      Evaluate correlation of TF expression and
                        target gene expression
create_triplet_distance_based
                        Map DNAm to target genes using distance
                        approaches, and TF to the DNAm region using
                        JASPAR2020 TFBS.
create_triplet_regulon_based
                        Map TF and target genes using regulon databases
                        or any user provided target-tf. Maps TF to the
                        DNAm region with TFBS using JASPAR2020 TFBS.
dna.met.chr21           TCGA-COAD DNA methylation matrix (beta-values)
                        for 38 samples (only chr21) retrieved from GDC
                        using TCGAbiolinks
filter_dnam_by_quant_diff
                        Select regions with variations in DNA
                        methylation levels above a threshold
filter_exp_by_quant_mean_FC
                        Select genes with variations above a threshold
filter_genes_zero_expression
                        Remove genes with gene expression level equal
                        to 0 in a substantial percentage of the samples
gene.exp.chr21.log2     TCGA-COAD gene expression matrix (log2 (FPKM-UQ
                        + 1)) for 38 samples (only chromosome 21)
                        retrieved from GDC using TCGAbiolinks
get_human_tfs           Access human TF from Lambert et al 2018
get_met_probes_info     Get HM450/EPIC manifest files from Sesame
                        package
get_promoter_avg        Summarize promoter DNA methylation beta values
                        by mean.
get_region_target_gene
                        Obtain target genes of input regions based on
                        distance
get_residuals           Get residuals from regression model
get_tf_ES               Calculate enrichment scores for each TF across
                        all samples using dorothea and viper.
get_tf_in_region        Get human TFs for regions by either scanning it
                        with motifmatchr using JASPAR 2020 database or
                        overlapping with TF chip-seq from user input
interaction_model       Fits linear models with interaction to triplet
                        data (Target, TF, DNAm), where DNAm is a binary
                        variable (samples in Q1 or Q4)
make_dnam_se            Transform DNA methylation array into a
                        summarized Experiment object
make_exp_se             Transform gene expression matrix into a
                        Summarized Experiment object
make_granges_from_names
                        Create a Granges object from a genmic region
                        string
make_names_from_granges
                        Create region name from Granges
methReg_analysis        Wrapper for MethReg functions
plot_interaction_model
                        Plot interaction model results
plot_stratified_model   Plot stratified model results
readRemap2022           Access REMAP2022 non-redundant peaks
stratified_model        Fits linear models to triplet data (Target, TF,
                        DNAm) for samples with high DNAm or low DNAm
                        separately, and annotates TF
                        (activator/repressor) and DNam effect over TF
                        activity (attenuate, enhance).
