This repository contains scripts for analysis and figure generation of the paper
Batra*, Arnold* et. al. The landscape of metabolic brain alterations in Alzheimer's disease (2022), Alzheimer's & Dementia. link
| Script name | Description |
|---|---|
| internal_functions.R | Internal customized functions. Will be sourced by other scripts |
| 1_metabolomics_preprocessing.R | ROS/MAP metabolomics preprocessing |
| 2_table1.R | ROS/MAP demographics table (Table 1 in manuscript) |
| 3_demographics_analysis.R | ROS/MAP demographics and PMI metabolomic association analysis |
| 4_metabolomics_association_analysis.R | ROS/MAP AD-traits metabolomic association analysis and conditional analysis |
| 5_beta_sex_apoe_analysis.R | ROS/MAP sex- and APOE4-stratified analysis |
| 6_mayo_analysis.R | Mayo metabolomic preprocessing and association analysis |
| 7_proteomics_analysis.R | ROS/MAP proteomic preprocessing, AD-traits association and conditional analysis |
| 8_figures.R | Panels of Figures 2, 3, 4 (Figures 1,5 and 6 were manually generated) |
| Folder | Description |
| input | Contains the input data to be used by the scripts |
| results | Will contain output files |
| Output files in results/ | Description |
| tmp* | Intermediate files used in follow-up scripts |
| supplementary* | Supplementary files from the paper |
| Figure* | Figure panels from the paper |
The data used in this paper can to be obtained from two sources: (1) Metabolomics data for the ROS/MAP and Mayo cohorts, clinical data for the Mayo cohort, and proteomics data for the ROS/MAP cohort are available via the AD Knowledge Portal (https://adknowledgeportal.org). The AD Knowledge Portal is a platform for accessing data, analyses, and tools generated by the Accelerating Medicines Partnership (AMP-AD) Target Discovery Program and other National Institute on Aging (NIA)-supported programs to enable open-science practices and accelerate translational learning. The data, analyses and tools are shared early in the research cycle without a publication embargo on secondary use. Data is available for general research use according to the following requirements for data access and data attribution (https://adknowledgeportal.org/DataAccess/Instructions). For access to content described in this manuscript see: http://doi.org/10.7303/syn26401311. (2) The full complement of clinical and demographic data for the ROS/MAP cohort are available via the Rush AD Center Resource Sharing Hub and can be requested at https://www.radc.rush.edu.
Input files for scripts: enzymes.xlsx, outcomes.xlsx, blsa_results.xlsx, medication_columns.xlsx are provided with content in the input folder.
Run scripts in sequence 1 to 8. Scripts 1 and 7 are time consuming, please read the comments in each file for more information. For script 8, a running Cytoscape session is needed to generate network files.
An interactive network view of AD associations from this study can be found here.