**This repository provides the analysis output for the pQTL study discussed in**
***H. Ruffieux, J. Carayol, R. Popescu, M. E. Harper, R. Dent, W. H. M. Saris, A. Astrup, A. C. Davison, J. Hager, and A. Valsesia. A fully joint Bayesian quantitative trait locus mapping of human protein abundance in plasma, PLOS Computational Biology, 16:e1007882, 2020.***
It is organized in two folders:
**1. LOCUS analysis output** - contains the posterior output obtained by the application of the joint Bayesian method LOCUS (Ruffieux et al., 2017) on the mass-spectrometry and SomaLogic QTL datasets, namely, each RData object contains:
- a matrix of posterior probabilities of associations between each SNP and each protein level;
- a vector of posterior mean for the pleiotropy parameter omega (one entry for each SNP).
**2. GEMMA analysis output** - contains the output obtained by the application of the univariate mixed model approach GEMMA (Zhou and Stephens, 2012) on the mass-spectrometry and SomaLogic QTL datasets for the Ottawa and DiOGenes cohorts, namely, each RData object contains a matrix of *p*-values for the associations between each SNP and each protein level (for the SomaLogic analysis, filtered *p*-values < 0.001 for size reasons).
