Score_adjust_PPI {COSINE}R Documentation

To adjust the score of the selected PPI sub-network using random sampling

Description

Randomly sample a large number of node-sets and edge-sets from the background PPI network to derive the null distribution of the scores for subnetworks with certain size, and to compute the adjusted scores for the selected sub-network

Usage

Score_adjust_PPI(scaled_node_score, scaled_edge_score, 
PPI, lam, subnet, num_random_sampling, best_score)

Arguments

scaled_node_score

The scaled F-statistics of each node(gene) in the network

scaled_edge_score

The scaled ECF-statistics of each edge in the network

PPI

A matrix with two columns containing the interacting gene pairs

lam

The weight parameter lambda used for the selection of this sub-network

subnet

A vector of the index of selected genes

num_random_sampling

Number of random subnetworks to be sampled

best_score

The original score of selected sub-network

Value

The adjusted score of the selected sub-network

Author(s)

Haisu Ma

Examples

data(scaled_node_score)
data(scaled_edge_score)
data(PPI)
data(set1_GA)
adj_Score<-Score_adjust_PPI(scaled_node_score,scaled_edge_score,
PPI,lam=0.1,subnet=set1_GA$Subnet[[1]],num_random_sampling=2,
best_score=set1_GA$Best_Scores[1])


[Package COSINE version 2.1 Index]