This package presents an improved analytical tool for prioritizing genes associated with diseases using gene network information. The DiSNEP package implemented the Disease-Specific Network Enhancement Prioritization (DiSNEP) framework. The DiSNEP framework first enhances a comprehensive gene network specifically for a disease through a diffusion process on a gene-gene similarity matrix derived from a disease omics data. The enhanced disease-specific gene network thus better reflects true gene interactions for the disease and may improve prioritizing disease-associated genes subsequently.
The package can be installed through: if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools") library("devtools") install_github("pfruan/DiSNEP")
The package DiSNEP depends on: R (>= 3.5.0), SMUT (>= 1.1), Rcpp (>= 0.12.3)
library(DiSNEP) data("s0") data("adjacency") data("signals")
res=diffus_vec(signals,se_post,type="pvalue", beta=0.75, iter=10, difference=1e-6, top=100)
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