get_dorothea {decoupleR} | R Documentation |
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
get_dorothea( organism = "human", levels = c("A", "B", "C"), weight_dict = list(A = 1, B = 2, C = 3, D = 4) )
organism |
Which organism to use. Only human and mouse 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. |
dorothea <- get_dorothea(organism='human', levels=c('A', 'B', 'C'))