Man pages for MethReg
Assessing the regulatory potential of DNA methylation regions or sites on gene transcription
| clinical | TCGA-COAD clinical matrix for 38 samples retrieved from GDC... |
| cor_dnam_target_gene | Evaluate correlation of DNA methylation region and target... |
| cor_tf_target_gene | Evaluate correlation of TF expression and target gene... |
| create_triplet_distance_based | Map DNAm to target genes using distance approaches, and TF to... |
| create_triplet_regulon_based | Map TF and target genes using regulon databases or any user... |
| dna.met.chr21 | TCGA-COAD DNA methylation matrix (beta-values) for 38 samples... |
| filter_dnam_by_quant_diff | Select regions with variations in DNA methylation levels... |
| 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... |
| gene.exp.chr21.log2 | TCGA-COAD gene expression matrix (log2 (FPKM-UQ + 1)) for 38... |
| 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... |
| get_tf_in_region | Get human TFs for regions by either scanning it with... |
| interaction_model | Fits linear models with interaction to triplet data (Target,... |
| make_dnam_se | Transform DNA methylation array into a summarized Experiment... |
| make_exp_se | Transform gene expression matrix into a Summarized Experiment... |
| make_granges_from_names | Create a Granges object from a genmic region string |
| make_names_from_granges | Create region name from Granges |
| MethReg | MethReg: functional annotation of DMRs identified in... |
| plot_interaction_model | Plot interaction model results |
| plot_stratified_model | Plot stratified model results |
| stratified_model | Fits linear models to triplet data (Target, TF, DNAm) for... |
