Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

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Documentation for package ‘MethReg’ version 1.19.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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 JASPAR2024 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
export_results_to_table	Format MethReg results table and export to XLSX file
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 2024 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).