Description Usage Arguments Value Examples
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.
1 2 | init_simulation_gene_net(base_correlation = 0.4,
change_correlation = 0.8, sample_size = 100, num_gene = 5000, change_gene_num=5)
|
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 |
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 |
1 2 3 4 5 6 7 | ## 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)
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