| File | Description |
|---|---|
| doc/ | Documents and auxiliary files |
| SomaLogic_analysis_plan.md | Analysis plan |
| SomaLogic.R | Generation of axuiliary files such as SomaLogic.list for a list of proteins |
| format.sh | GWAS summary statistics reformat using GNU Parallel, e.g., format.sh FHS |
| format.sb | SLURM scripts |
| format.subs | Processing of a particular study and array job |
| list.sh | Generation of received and output file lists and directories |
| metal.sh | Generation and execution of individual METAL entries |
| metal.sb | SLURM routine |
| QCGWAS.sb | QCGWAS -- SLURM |
| QCGWAS.R | QCGWAS -- R |
| clump.sh | PLINK clumping |
| clump.sb | SLURM routine |
| qml.sh | Q-Q, Manhattan (qqman.R) and LocusZoom plots |
| qml.sb | SLRUM routine |
The workflows involve the following components,
- Data are downloaded from the Box server to dedicated directories; as noted in box.md.
- Available entries are catalogued in a list, as done by
list.*. - GWAS summary statistics associated with the list are reformatted by
format.*according to the analysis plan. - When necessary, the summary statistics are examined with R/QCGWAS.
- Batch scripts for metal analysis are then generated and executed with
metal.*. - Downstream analysis according to plan.
The repository can be downloaded locally with
git clone https://github.com/jinghuazhao/SomaLogicSomaLogic, wiki, GenomeWeb reports, the 1129 assay (1129.tsv, derived from SSM-011-Rev-11-SOMAscan-Assay-V1-1k-Content.pdf), 1310 assay (1310.tsv, derived from SSM-045-REV-1-SOMAscan-Assay-1-3k-Content-1.pdf, and Rev-2), and SOMAscan Proteomic Assay Technical Whie Paper.
Behar M (2018). Proteomics might have saved my mother’s life and it may yet save mine. The New York Times Magazine, https://www.nytimes.com/interactive/2018/11/15/magazine/tech-design-proteomics.html, also here (PDF).
Ganz P, et al. (2016). Development and validation of a protein-based risk score for cardiovascular outcomes among patients with stable coronary heart disease. JAMA 315(23):2532-2541. doi:10.1001/jama.2016.5951, https://jamanetwork.com/journals/jama/fullarticle/2529627
Suhre K, et al. (2017). Connecting genetic risk to disease end points through the human blood plasma proteome. Nat Commun 8, 14357, https://doi.org/10.1038/ncomms14357 (https://metabolomics.helmholtz-muenchen.de/pgwas/).
Sun BB, et al. (2018). Genomic atlas of the human plasma proteome. Nature 558: 73–79 (http://www.phpc.cam.ac.uk/ceu/proteins/).