README.md

In lwa19/ICN: Use Interconnected Communities Network (ICN) to characterize population subgroup features.

ICN

Interconnected Communities Network

The goal of this project is to apply the Interconnected Communities Network (ICN) to cancer patient data from The Cancer Genome Atlas (TCGA) project in order to identify similar cancer types and potential subtypes. The writeup of our results can be found here. A minimum working example of the ICN framework and analysis pipeline can be found in the vignettes. Our methods are implemented into an R package ICN, which can be installed using the following command:

Installation Guide

library(devtools)
install_github("lwa19/ICN", build_vignettes = TRUE)

Vignettes: Minimum Working Example

You may access all the vignettes and further analyses by running:

browseVignettes('ICN')

file structure

ICN
| R/                            - all of the written R functions and scripts
  | Auxiliary.R                 - all of the helper functions (inaccessible to users)
  | InterCon.R                  - R package function -- identification of significant edges
  | KLtest.R                    - R package function -- calculating and testing interconnectedness between communities using KL divergence
  | NICE_fast_cut.R             - R package function -- construct communities using K-means clustering
  | NICE_simulation.R           - R script -- simulate data and cluster using NICE algorithm
  | step1.R                     - R script -- execute NICE algorithm for input correlation matrix
  | step2.R                     - R script -- process NICE cluster output and perform KL divergence test between communities
  | step3.R                     - R script -- Detect interconnected edges within two communities
  | utils.R                     - R package function -- post processing function for NICE cluster output
| examples/                     - saved simulation data
  | corr.rds                    - simulated correlation matrix
  | nice.rds                    - NICE cluster output of simulated data
| vignettes/                    - R package vignettes
  | mwe.rmd                     - A minimum working example using simulation data

Group Members

Ziming Huang ([e-mail])

Xin Luo ([e-mail])

Yao Song ([e-mail])

Lijia Wang ([e-mail])

Acknowledgements

We are grateful for the instruction and help from Professor Hui Jiang and the GSI Jingyi Zhai, and the materials taught in the course BIOSTAT 625.

lwa19/ICN documentation built on Dec. 23, 2021, 10:23 p.m.