README.md

In Kaiyu-W/DNBr: Compute the Dynamic Network Biomarkers (DNB) model

DNBr

This code is written by R, to compute the Dynamic Network Biomarkers(DNB) model developed by ChenLab in CAS, China.

If you're interested in this subject, please - go to http://sysbio.sibcb.ac.cn/sysbio/cb/chenlab/LuonanChen.htm or - email [e-mail] to let us know.

To install this package, use the following command in R:

devtools::install_github("Kaiyu-W/DNBr")

More details see the codes by vignette("DNBr") or ?DNBr::function in R, please.

Log: - Add choice high_cutoff = -1 for DNBcompute() to skip selecting highly variable genes. - Add parameter force_allgene for DNBfilter() to control which genes are used as background.

• Note that,
• To stay consistent with DNBcompute(), DNBfilter(force_allgene = FALSE) as default.
• There may be some missing genes when DNBfilter(force_allgene = FALSE) because of different high variable genes among groups, and those missing ones will later be removed from modules during computation. Use DNBcompute(..., high_cutoff = -1) to avoid this.
• Use DNBfilter(..., force_allgene = TRUE) to re-produce the output by early version.

Example:

library(DNBr)
data(data.example)
data(meta.example)

a <- DNBcompute(data.example, meta.example)
b <- DNBfilter(a, ntop = 5, force_allgene = TRUE)
DNBplot(b, show = TRUE, save_pdf = FALSE)

Kaiyu-W/DNBr documentation built on April 27, 2024, 10:09 a.m.