examples/troubleshooting_example.R

In taylorpourtaheri/nr: Node prioritization optimizer

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

# load all package functions
devtools::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

# define globals
deg <- myc_de
edge_conf_score_min <- 950
logFC_min <- 1.5
pvalue_max <- 0.05
causal_gene_symbol <- 'MYC'
method <- 'betweenness'
final_results <- c()
export_network <- FALSE
n_sim <- 9999
sim_method <- 'jaccard'
weighted <- TRUE

# network generation ------------------------------------------------------

# generate protein association network
string_db <- STRINGdb::STRINGdb$new(version="11",
                                    species=9606,
                                    score_threshold=edge_conf_score_min)
ppi <- string_db$get_graph()

# map DEA results onto ppi network
ppi_painted <- df_to_vert_attr(graph=ppi, df=deg, common="STRING_id",
                               attr_name = c("Symbol", "ID", "logFC", "AveExpr",
                                             "t", "P.Value", "adj.P.Val", "B"))