Publication data

CpG methylation prediction models (.db files, ready for use with S-PrediXcan) from Fryett et al. (2022) "Investigating the prediction of CpG methylation levels from SNP genotype data to help elucidate relationships between methylation, gene expression and complex traits" Genetic Epidemiology 46(8):629-643. doi: 10.1002/gepi.22496.

Understanding Society models (recommended)
Understanding Society covariance file

ARIES models
ARIES covariance file

Note that the covariance files are only required for summary statistics based analysis (MetaXcan/SPrediXcan) and not for individual level data based PrediXcan-type analysis.

Example commands for running the analysis:

SPrediXcan.py \
--model_db_path UnderstandingSociety.predictionmodels.db \
--covariance UnderstandingSociety.covariancefile.txt.gz \
--gwas_folder PBC-META2018/SUMMARY_STATS_UPDATED_AUG2019 \
--gwas_file_pattern "EuropeanSumStats_GWAS_Catalog.tsv" \
--snp_column variant_id \
--effect_allele_column effect_allele \
--non_effect_allele_column other_allele \
--beta_column beta \
--se_column standard_error \
--output_file resultsUS.csv