This webpage summarizes the analyses published in Revez et al. 2020 Nature Communications. It includes the following sections (documented with code):
- Pheno: Section describing:
- How data were download and extracted for analyses
- Exploratory analyses performed
- How the phenotype files used in the GWAS section were created
- GWAS: Section describing how genome-wide association (GWA) analyses were performed and the results of those analyses. Three classical GWA analyses were conducted:
- PLINK GWAS - on unrelated individuals with European ancestry
- FastGWA - on individuals with European ancestry
- BOLT-LMM - on individuals with European ancestry
- BMI: Section describing the analyses conducted to assess the relationship between vitamin D and body mass index (BMI).
- Meta-analysis: Section with meta-analysis of our GWAS results with those from the SUNLIGHT Consortium
- Heritability: Section where we estimate the proportion of phenotypic variability explained by genetic variants.
- Annotation: Section with follow-up analyses on GWA results.
- SMR: Section with summary Mendelian randomization (SMR) analyses, which integrate our GWAS results with results from expression (eQTL) and methylation (mQTL) quantitative trait loci GWAS results
- GSMR: Section with results from our generalized summary Mendelian randomization (GSMR) analyses, which test for putative causal association between vitamin D and other traits
- Stratified GWAS: Section with GWAS on vitamin D levels measured in (1) Summer, and (2) Winter
- vQTL: Section with variance QTL (vQTL) GWA analysis on unrelated individuals with European ancestry
Note: This document is hosted in this github repository