generateTFList: 'generateTFList'

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

Description

assignPROGENyScores

Usage

generateTFList(df = TF_activities, top = 50, 
                            access_idx = 1)

Arguments

df	the inferred TF activities from viper function
top	the top TF's with highes absolute activity values to be generated for the CARNIVAL analysis. Default set to top=50. When considering all TF's, then top="all"
access_idx	index of the sample to consider (default set to access_idx = 1 - generate table for the first TF sample (if all, set access_idx = 1:ncol(df)))

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)
library(viper)
library(progeny)

expr <- as.matrix(read.csv(system.file("extdata", "human_input.csv", 
                                              package = "progeny"), 
                                              row.names = 1))

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)

TF_activities = as.data.frame(viper::viper(eset = expr, 
                                           regulon = regulons, nes = T, 
                                           method = 'none', minsize = 4, 
                                           eset.filter = F))

tfList <- generateTFList(df = TF_activities, top = "all", 
                            access_idx = 1)

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