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Supplementary materials for the article 'Network hub detection using the entire solution path information'.

License: GNU General Public License v3.0

R 100.00%

mdsd_supplementary's Introduction

MDSD_supplementary

Supplementary materials for the article 'Network hub detection using the entire solution path information'.

See also https://github.com/markkukuismin/MDSD.

Dependencies

install.packages(c("igraph", "ggplot2", "huge", "hglasso", "tidyverse", "gridExtra"))

Package space package is removed from the CRAN repository (last visit 20/2/2024) and must be installed using the tar.gz file.

Packages DESeq2 and genefilter are available on Bioconductor,

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(c("DESeq2", "genefilter"))

Main article Figures

Use these scripts to reproduce Figures of the article,

  • manuscript_figures/Fig1.R: Main article Figure 1.
  • manuscript_figures/Supp_Fig2_and_Fig3.R: Main article Figure 2.
  • real_data_examples/Maize_ligule/Maize_ligule_hglasso.R: Main article Figure 3.

Simulations

Use these scripts to reproduce the simulations results reported in the main article and Supplementary materials,

  • simulations/simulations_lossy_screening.R: Lossy screening rule of the sample correlation matrix simulations.
  • simulations/simulations_hglasso.R: Hub glasso simulations.
  • simulations/simulations_local_hub_screening.R: Firouzi & Hero (2013) hub screening method simulations.
  • simulations/simulations_space.R: space simulations.

Real data example

Use the script to reproduce the real data example reported in the main article. The data set is publicly available at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61333

  • Maize_ligule_hglasso.R: Derive a gene co-expression network to detect hub genes of Maize ligule data.

mdsd_supplementary's People

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