Man pages for MethReg
Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

clinicalTCGA-COAD clinical matrix for 38 samples retrieved from GDC...
cor_dnam_target_geneEvaluate correlation of DNA methylation region and target...
cor_tf_target_geneEvaluate correlation of TF expression and target gene...
create_triplet_distance_basedMap DNAm to target genes using distance approaches, and TF to...
create_triplet_regulon_basedMap TF and target genes using regulon databases or any user...
dna.met.chr21TCGA-COAD DNA methylation matrix (beta-values) for 38 samples...
filter_dnam_by_quant_diffSelect regions with variations in DNA methylation levels...
filter_exp_by_quant_mean_FCSelect genes with variations above a threshold
filter_genes_zero_expressionRemove genes with gene expression level equal to 0 in a...
gene.exp.chr21.log2TCGA-COAD gene expression matrix (log2 (FPKM-UQ + 1)) for 38...
get_human_tfsAccess human TF from Lambert et al 2018
get_met_probes_infoGet HM450/EPIC manifest files from Sesame package
get_promoter_avgSummarize promoter DNA methylation beta values by mean.
get_region_target_geneObtain target genes of input regions based on distance
get_residualsGet residuals from regression model
get_tf_ESCalculate enrichment scores for each TF across all samples...
get_tf_in_regionGet human TFs for regions by either scanning it with...
interaction_modelFits linear models with interaction to triplet data (Target,...
make_dnam_seTransform DNA methylation array into a summarized Experiment...
make_exp_seTransform gene expression matrix into a Summarized Experiment...
make_granges_from_namesCreate a Granges object from a genmic region string
make_names_from_grangesCreate region name from Granges
MethRegMethReg: functional annotation of DMRs identified in...
plot_interaction_modelPlot interaction model results
plot_stratified_modelPlot stratified model results
stratified_modelFits linear models to triplet data (Target, TF, DNAm) for...
MethReg documentation built on Nov. 8, 2020, 8:01 p.m.