init_simulation_gene_net: Create a random network for simulation

In ilab/DNLC: Differential Network Local Consistency Analysiss

Description

This function will create a network for DNLC. This function will change correlation of chosen genes and its one hop neighbor between treatment groups to simulate LMI changes.

Usage

init_simulation_gene_net(base_correlation = 0.4, 
    change_correlation = 0.8, sample_size = 100, num_gene = 5000, change_gene_num=5)

Arguments

base_correlation	base correlation of network
change_correlation	change correlation for selected genes
sample_size	multi size of patient data
num_gene	gene number in the network
change_gene_num	number of genes around which the correlation structure is to be changed

Value

lmi_matrix	matrix of local moran's I data
patient_matrix	matrix of patient data
neigh_list	id of changed gene.
gene_graph	igraph object of gene network
gene_expr	gene expression data matirx

Examples

## Not run: 
simulation <- init_simulation_gene_net()
t_data = DNLC_statistics(simulation$gene_graph, simulation$gene_expr,
  simulation$patient_matrix, lmi_data = simulation$lmi_matrix)
fdr_result <- gene_fdrtest(t_data)
sig_genes <- significant_genes(fdr_obj = fdr_result, thres = 0.2)
## End(Not run)

ilab/DNLC documentation built on May 5, 2019, 5:52 p.m.