calculate_p0: Function to calculate the p0 vector used in Random Walk with...

In DTSEA: Drug Target Set Enrichment Analysis

Function to calculate the p0 vector used in Random Walk with Restart (RwR)

Description

The function provides a reliable approach to generating a p0 vector.

Usage

calculate_p0(nodes, disease)

Arguments

nodes	The nodes variable can either accept the igraph object or the nodes vector.
disease	The disease variable must specify the disease-affected nodes in a short vector.

Value

The resulting p0 vector.

Examples

library(DTSEA)
library(dplyr)

# Load the data
data("example_disease_list", package = "DTSEA")
data("example_drug_target_list", package = "DTSEA")
data("example_ppi", package = "DTSEA")

# Compute the p0 vector
p0 <- calculate_p0(nodes = example_ppi, disease = example_disease_list)

# You can decrease the order of the p0 to get the most affected nodes.
p0 <- sort(p0, decreasing = TRUE) %>%
  names() %>%
  head(10)

# If you have obtained the supplemental data, then you can compute the p0
# in the real data set

# supp_data <- get_data(c("graph", "disease_related"))
# p0 <- calculate_p0(nodes = supp_data[["graph"]],
#                    disease = supp_data[["disease_related"]])

DTSEA documentation built on Nov. 10, 2022, 5:09 p.m.