init_simulation_gene_net: Create a random network for simulation

Description Usage Arguments Value Examples

View source: R/DNLC.R

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

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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

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## 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)

DNLC documentation built on May 30, 2017, 5:52 a.m.