get_seeds_score {ssMutPA}

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)