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 |
MethReg: functional annotation of DMRs identified in epigenome-wide association studies |
methReg_analysis |
Wrapper for MethReg functions |
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 samples with high DNAm or low DNAm separately, and annotates TF (activator/repressor) and DNam effect over TF activity (attenuate, enhance). |