Analysis code for "Streptococcus species abundance in the gut is linked to subclinical coronary atherosclerosis in 8973 participants from the SCAPIS cohort" by Sayols-Baixeras et al.

scripts

Contains the analysis scripts.

• process_data.R has been used to process the data for the analyses performed in SCAPIS.
• run_alpha_models.R has been used to generate the alpha diversity analysis results.
• run_beta_models.R has been used to generate the beta diversity analysis results.
• run_alpha_stepwise_models.R has been used to generate the alpha diversity analysis results for the basic model, after adding each covariate from the main model separately.
• run_beta_stepwise_models.R has been used to generate the beta diversity analysis results for the basic model, after adding each covariate from the main model separately.
• run_basic_and_main_models.R has been used to generate the the basic and main model analysis results for the association between species and CACS.
• run_sensitivity_models.R has been used to generate the sensitivity analysis results.
• run_gsea.R has been used to generate the enrichment analysis results for taxonomic genera.
• run_GMM_models.R has been used to generate the the basic and main model analysis results for the association between gut metabolic modules and CACS.
• run_inflammation_models.R has been used to generate the analysis results for the inflammation markers.
• process_mods.R has been used to process the data for the analyses performed in MOS/MODS.
• run_oral_models.R has been used to generate the oral microbiome analysis results.
• run_influent_mixed_model.R has been used to generate the influential observation analysis results for the association between species and CACS.
• run_influent_mixed_model_GMM.R has been used to generate the influential observation analysis results for the association between gut metabolic modules and CACS.
• Random_effects_ordinal.do has been used to generate the sensitivity analysis results for the association between species and CACS category using ordinal regression.
• Random_effects_logistic2.do has been used to generate the analysis results for the other binary atherosclerosis measurements.
• Random_effects_ordinal2.do has been used to generate the analysis results for the other ordinal atherosclerosis measurements.
• CombineResults.do has been used to combine all Stata analysis results.

tables

Contains the tables generated by the analysis scripts. The tables from the influential_mixed scripts are located in a subfolder named influential/.

old

Contains the previous versions of the analysis code.