Notes
See also https://github.com/jinghuazhao/Believe/tree/master/docs/T2D for additional files.
BGLR/
This folder contains data and R script for Crossa et al. (2020), see below.
brms/
At this stage, the demonstrate how to run a SLURM job on CSD3.
Change account and $USER appropriately.
- Script, csd3.sb
- Error report: _csd3.e
- Output report: _csd3.o
- Plot: brms-fit3.pdf
ldsc
This implements LD-score regression, which is available from CSD3 by module load ceuadmin/ldsc as indicated here, https://cambridge-ceu.github.io/csd3/Python/ldsc.html.
Mixed effects Cox models
- kinship, in here, CRAN archive and GitHub.
- coxme, https://cran.r-project.org/web/packages/coxme/index.html, which includes updates on kinship.
- coxmeg, https://github.com/lhe17/coxmeg, which is an update to CRAN archive.
All are R packages available under ceuadmin/R modules.
References
Crossa J, Montesinos-López OA, Pérez-Rodríguez P, Costa-Neto G, Fritsche-Neto R, Ortiz R, Martini JWR, Lillemo M, Montesinos-López A, Jarquin D, Breseghello F, Cuevas J, Rincent R. Genome and Environment Based Prediction Models and Methods of Complex Traits Incorporating Genotype × Environment Interaction. Methods Mol Biol. 2022;2467:245-283. doi: 10.1007/978-1-0716-2205-6_9. PMID: 35451779, https://link.springer.com/protocol/10.1007/978-1-0716-2205-6_9.
He L, Kulminski AM. Fast Algorithms for Conducting Large-Scale GWAS of Age-at-Onset Traits Using Cox Mixed-Effects Models. Genetics. 2020 May;215(1):41-58. doi: 10.1534/genetics.119.302940. Epub 2020 Mar 4. Erratum in: Genetics. 2020 Aug;215(4):1191. PMID: 32132097; PMCID: PMC7198273, https://academic.oup.com/genetics/article/215/1/41/5930490.