get_dorothea: DoRothEA gene regulatory network.

In saezlab/decoupleR: decoupleR: Ensemble of computational methods to infer biological activities from omics data

DoRothEA gene regulatory network.

Description

Wrapper to access DoRothEA gene regulatory network. DoRothEA is a comprehensive resource containing a curated collection of transcription factors (TFs) and their target genes. Each interaction is weighted by its mode of regulation (either positive or negative) and by its confidence level

Usage

get_dorothea(
  organism = "human",
  levels = c("A", "B", "C"),
  weight_dict = list(A = 1, B = 2, C = 3, D = 4)
)

Arguments

organism	Which organism to use. Only human, mouse and rat are available.
levels	List of confidence levels to return. Goes from A to D, A being the most confident and D being the less.
weight_dict	Dictionary of values to divide the mode of regulation (-1 or 1), one for each confidence level. Bigger values will generate weights close to zero.

Examples

dorothea <- get_dorothea(organism='human', levels=c('A', 'B'))

saezlab/decoupleR documentation built on Oct. 21, 2024, 8:47 a.m.