examples/propagation_pipeline_example.R

In taylorpourtaheri/nr: Node prioritization optimizer

# load relevant packages
library(STRINGdb)
library(igraph)
library(ggplot2)
library(ggnetwork)
library(dplyr)
library(glue)
library(devtools)

# load all package functions
load_all()

# read differential expression data (annotated with gene symbols)
de_string <- readRDS('data/de_string_v11.RDS')

# select MYC condition as an example
myc_de <- de_string$MYC

# call wrapper
results <- propagation_pipeline(deg = myc_de,
                            edge_conf_score_min = 950,
                            logFC_min = 2.0,
                            pvalue_max = 0.25,
                            method = 'ml',
                            causal_gene_symbol = 'MYC',
                            export_network = FALSE,
                            sim_method = 'jaccard',
                            n_sim = 9999,
                            weighted = TRUE)

# # plot output
# set.seed(4)
# plot_graph(results[['network']], method = 'weighted_score', gene_list = c('MYC'))
# ggsave('test2.png', width = 12, height = 12)