createRegulonList: 'createRegulonList'

In saezlab/CARNIVAL-Bioconductor-Dev: A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

Description

assignPROGENyScores

Usage

createRegulonList(regulon_table = regulon_table)

Arguments

regulon_table

the regulon matrix with columns the source, sign and target of the TF interaction.

Value

This function creates a regulon list similar to vipper from an interaction matrix. The interaction matrix contains as columns the source, sign and the target of the interaction

Author(s)

Enio Gjerga

Examples

library(CARNIVAL)
library(OmnipathR)

regulon_df <- 
  import_TFregulons_Interactions(select_organism = 9606)

regulon_df <- 
  regulon_df[which((regulon_df$is_stimulation+regulon_df$is_inhibition)==1), ]

regulon_table <- matrix(data = , nrow = nrow(regulon_df), ncol = 3)
regulon_table[, 1] <- regulon_df$source_genesymbol
regulon_table[which(regulon_df$is_stimulation==1), 2] = "1"
regulon_table[which(regulon_df$is_inhibition==1), 2] = "-1"
regulon_table[, 3] <- regulon_df$target_genesymbol

regulons <- createRegulonList(regulon_table = regulon_table)

saezlab/CARNIVAL-Bioconductor-Dev documentation built on Aug. 30, 2020, 2:39 p.m.