Published December 14, 2018
| Version v1
Software
Open
Whole-genome sequencing analysis
Authors/Creators
- 1. Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
Description
This repository contains R scripts for risk score analysis and annotation clustering in An et al. Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder. Science 362, eaat6576 (2018). DOI: 10.1126/science.aat6576.
The raw data are not included in this repository. For data generation, please refer to https://github.com/sanderslab/WGS-pipeline. The latest version of this code is available at https://github.com/lingxuez/WGS-Analysis.
- Risk score analysis
- Compute the predictive R2 of rare annotations:
risk_score/predictive_r2.R - Compute the p-value:
risk_score/significance_r2.R
- Compute the predictive R2 of rare annotations:
- Annotation clustering
- Spectral clustering of annotation categories:
clustering/clustering.R
- Spectral clustering of annotation categories:
- Network analysis
- Forming the graph and determining the significance of each cluster of nodes:
network/network.R - Because many custom functions are needed for this step, a supplemental R package is located in
network/supernodeWGSto encapsulate all the needed functions
- Forming the graph and determining the significance of each cluster of nodes: