diffus_matrix: Network enhancement by diffusion process.

In pfruan/DiSNEP: DiSNEP: a Disease-Specific Enhancement for gene Network Enhancement to improve Prioritizing candidate disease genes

Network enhancement by diffusion process.

Description

Enhances a comprehensive gene network for a disease using a gene-gene similarity network derived from a type of omics data of the disease that reflects correlations/interactions between genes for the disease.

Usage

diffus_matrix(s0, adjacency, alpha=0.75,iter=10, difference=1e-6)

Arguments

s0	The original general gene network.
adjacency	A gene-gene similarity network derived from a type of omics data of a disease.
alpha	A regularization parameter representing weights for signal sources where α = 0 means no disease-specific enhancement.
iter	Number of iterations.
difference	A parameter for converenge.

Value

The enhanced disease-specific network.

References

DiSNEP: a Disease-Specific gene Network Enhancement to improve Prioritizing candidate disease genes (2020), Peifeng Ruan, Shuang Wang.

Examples

#enhance the general network s0 into a disease specific network by diffusion on similarity network generated from disease omics data.
se=diffus_matrix(s0,adjacency)

#denoise the enhanced network and make it binary and symmetric.
se_post=post_process(se)

#prioritize the disease association signals.
res=diffus_vec(signals,se_post,"pvalue")

pfruan/DiSNEP documentation built on Oct. 12, 2023, 3:29 p.m.