get_tf_ES: Calculate enrichment scores for each TF across all samples...

In TransBioInfoLab/MethReg: Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

Calculate enrichment scores for each TF across all samples using dorothea and viper.

Description

Calculate enrichment scores for each TF across all samples using dorothea and viper.

Usage

get_tf_ES(exp, min.confidence = "B", regulons)

Arguments

exp	Gene expression matrix with gene expression counts, row as ENSG gene IDS and column as samples
min.confidence	Minimun confidence score ("A", "B","C","D", "E") classifying regulons based on their quality from Human DoRothEA database. The default minimun confidence score is "B"
regulons	DoRothEA regulons in table format. Same as run_viper. If not specified Bioconductor (human) dorothea regulons besed on GTEx will be. used dorothea_hs.

Value

A matrix of normalized enrichment scores for each TF across all samples

Examples

gene.exp.chr21.log2 <- get(data("gene.exp.chr21.log2"))
tf_es <- get_tf_ES(gene.exp.chr21.log2)

TransBioInfoLab/MethReg documentation built on July 28, 2023, 9:17 p.m.