get_seeds_score: Calculate the local wight of seed nodes.

In ssMutPA: Single-Sample Mutation-Based Pathway Analysis

Calculate the local wight of seed nodes.

Description

The function 'get_seeds_score' is used to calculate the local wight of seed nodes in a single sample.

Usage

get_seeds_score(net_data, seed, mut_gene, BC_Num, cut_point = 0)

Arguments

net_data	A list of the PPI network information, including nodes and edges.
seed	A vector containing the gene symbols of the seed nodes.
mut_gene	A vector containing the gene symbols of the mutated genes in a single sample.
BC_Num	Number of background genes.
cut_point	The threshold of indicator function.

Value

A data frame containing the weight of seed nodes.

Examples

#load the data
net_path <- system.file("extdata","ppi_network.Rdata",package = "ssMutPA")
load(net_path)
data(mut_status)
seed<-intersect(names(mut_status[,1])[which(mut_status[,1]!=0)],igraph::V(ppi_network)$name)
mut_gene<-intersect(names(mut_status[,1])[which(mut_status[,1]!=0)],igraph::V(ppi_network)$name)
#perform the function `get_seeds_score`.
Seeds_Score<-get_seeds_score(net_data=ppi_network,seed=seed,mut_gene,BC_Num=12436,cut_point=0)

ssMutPA documentation built on Oct. 16, 2024, 1:06 a.m.