Score_adjust_PPI: To adjust the score of the selected PPI sub-network using...

Description Usage Arguments Value Author(s) Examples

View source: R/Score_adjust_PPI.R

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

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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

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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])

COSINE documentation built on May 1, 2019, 10:21 p.m.