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prioGene: Prioritize candidate genes for complex non-communicable diseases

:writing_hand: Authors

Erqiang Hu

College of Bioinformatics Science and Technology, Harbin Medical University

:arrow_double_down: Installation

Get the development version from github:

if(!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("huerqiang/prioGene")

Or the released version from CRAN:

install.packages("prioGene")

Common operations on prioGene

library(prioGene)

1. Construction of disease related networks

The function deal_net could get a disease-related network by retaining disease-causing genes and their One-step interaction neighbors in a human biological network. The parameter net means a human biological network, a matrix of two columns. The parameter dise_gene means a one-column-matrix of gene symbols obtained from the OMIM database or other disease-related databases. They need to be provided by the users. We provide examples separately in the package: prioGene::net and prioGene::dise_gene.

net_disease <- deal_net(net,dise_gene)

2. Calculation of network weights

These five functions form a pipeline to weight the nodes and edges of the network based on functional information. GO function annotation information comes from org.Hs.eg.db.

genes_mat <- get_gene_mat(net_disease)
terms_mat <- get_term_mat(net_disease)
net_disease_term <- get_net_disease_term(genes_mat,net_disease)
node_weight <- get_node_weight(genes_mat)
edge_weight <- get_edge_weight(net_disease_term,terms_mat)

3. Prioritization of candidate genes

The prioritization of candidate genes was performed based on disease risk scores of each gene obtained from an iteration process considering disease risks transferred between genes.

R_0<- get_R_0(dise_gene,node_weight,f=1)
result <- get_R(node_weight, net_disease_term, bet = 0.5, R_0 = R_0, threshold = 10^(-9))

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.