├── LICENSE ├── README.md ├── data ├── .gitignore ├── available_outcomes_Nov2017.RData └── gwas_catalog_Nov2017.RData ├── images ├── database.png ├── database.pptx ├── ldl-chd.png ├── pleiotropy_models.pdf ├── pleiotropy_models.png ├── sensitivity_boxes │ ├── LDL_cholesterol-Alzheimersdisease.png │ ├── LDL_cholesterol-Bodyfat.png │ ├── LDL_cholesterol-Bodymassindex.png │ ├── LDL_cholesterol-Chronotype.png │ ├── LDL_cholesterol-Coronaryheartdisease.png │ ├── LDL_cholesterol-Fastingproinsulin.png │ ├── LDL_cholesterol-Fathersageatdeath.png │ ├── LDL_cholesterol-Inspectiontime.png │ ├── LDL_cholesterol-Myocardialinfarction.png │ ├── LDL_cholesterol-Obesityclass1.png │ ├── LDL_cholesterol-Overweight.png │ ├── LDL_cholesterol-Parentsageatdeath.png │ ├── LDL_cholesterol-Sleepduration.png │ ├── LDL_cholesterol-Top1survival.png │ ├── LDL_cholesterol-Type2diabetes.png │ ├── LDL_cholesterol-Waistcircumference.png │ ├── LDL_cholesterol-Waisttohipratio.png │ ├── Triglycerides-Adiponectin.png │ ├── Triglycerides-Alzheimersdisease.png │ ├── Triglycerides-Asthma.png │ ├── Triglycerides-Coronaryheartdisease.png │ ├── Triglycerides-Correctedinsulinresponse.png │ ├── Triglycerides-Depressivesymptoms.png │ ├── Triglycerides-Extremewaisttohipratio.png │ ├── Triglycerides-Formervscurrentsmoker.png │ ├── Triglycerides-Gout.png │ ├── Triglycerides-Height.png │ ├── Triglycerides-Insulindispositionindex.png │ ├── Triglycerides-Insulinlikegrowthfactor1.png │ ├── Triglycerides-Microalbuminuria.png │ ├── Triglycerides-Myocardialinfarction.png │ ├── Triglycerides-Plasmacortisol.png │ ├── Triglycerides-Primarybiliarycirrhosis.png │ ├── Triglycerides-Waisttohipratio.png │ ├── pbc-triglycerides.png │ ├── supfig3.docx │ ├── supfig3.pdf │ ├── supfig3.rmd │ └── template.rmd └── volcano │ ├── drug_proxies_volcano_boxes.png │ ├── volcano_boxes.png │ └── volcano_boxes_ldl.png ├── results ├── lpa_ldl_trigs.RData └── mr_ivw_phewas_clump2.txt ├── scripts ├── PheWAS.R ├── figure_sensitivity_boxes.R ├── figure_volcano_plots.R ├── ldl-chd.R ├── pleiotropy_model_plots.R ├── run_mr.R └── tables.R └── tables ├── drug_prediction.csv ├── drug_proxy_results.csv ├── instruments.csv ├── mr_results.csv └── study.csv /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/README.md -------------------------------------------------------------------------------- /data/.gitignore: -------------------------------------------------------------------------------- 1 | mrbase.oauth 2 | -------------------------------------------------------------------------------- /data/available_outcomes_Nov2017.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/data/available_outcomes_Nov2017.RData -------------------------------------------------------------------------------- /data/gwas_catalog_Nov2017.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/data/gwas_catalog_Nov2017.RData -------------------------------------------------------------------------------- /images/database.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/database.png -------------------------------------------------------------------------------- /images/database.pptx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/database.pptx -------------------------------------------------------------------------------- /images/ldl-chd.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/ldl-chd.png -------------------------------------------------------------------------------- /images/pleiotropy_models.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/pleiotropy_models.pdf -------------------------------------------------------------------------------- /images/pleiotropy_models.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/pleiotropy_models.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Alzheimersdisease.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Alzheimersdisease.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Bodyfat.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Bodyfat.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Bodymassindex.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Bodymassindex.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Chronotype.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Chronotype.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Coronaryheartdisease.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Coronaryheartdisease.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Fastingproinsulin.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Fastingproinsulin.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Fathersageatdeath.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Fathersageatdeath.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Inspectiontime.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Inspectiontime.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Myocardialinfarction.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Myocardialinfarction.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Obesityclass1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Obesityclass1.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Overweight.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Overweight.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Parentsageatdeath.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Parentsageatdeath.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Sleepduration.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Sleepduration.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Top1survival.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Top1survival.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Type2diabetes.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Type2diabetes.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Waistcircumference.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Waistcircumference.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/LDL_cholesterol-Waisttohipratio.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/LDL_cholesterol-Waisttohipratio.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Adiponectin.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Adiponectin.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Alzheimersdisease.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Alzheimersdisease.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Asthma.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Asthma.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Coronaryheartdisease.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Coronaryheartdisease.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Correctedinsulinresponse.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Correctedinsulinresponse.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Depressivesymptoms.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Depressivesymptoms.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Extremewaisttohipratio.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Extremewaisttohipratio.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Formervscurrentsmoker.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Formervscurrentsmoker.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Gout.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Gout.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Height.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Height.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Insulindispositionindex.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Insulindispositionindex.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Insulinlikegrowthfactor1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Insulinlikegrowthfactor1.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Microalbuminuria.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Microalbuminuria.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Myocardialinfarction.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Myocardialinfarction.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Plasmacortisol.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Plasmacortisol.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Primarybiliarycirrhosis.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Primarybiliarycirrhosis.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/Triglycerides-Waisttohipratio.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/Triglycerides-Waisttohipratio.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/pbc-triglycerides.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/pbc-triglycerides.png -------------------------------------------------------------------------------- /images/sensitivity_boxes/supfig3.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/supfig3.docx -------------------------------------------------------------------------------- /images/sensitivity_boxes/supfig3.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/supfig3.pdf -------------------------------------------------------------------------------- /images/sensitivity_boxes/supfig3.rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/supfig3.rmd -------------------------------------------------------------------------------- /images/sensitivity_boxes/template.rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/sensitivity_boxes/template.rmd -------------------------------------------------------------------------------- /images/volcano/drug_proxies_volcano_boxes.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/volcano/drug_proxies_volcano_boxes.png -------------------------------------------------------------------------------- /images/volcano/volcano_boxes.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/volcano/volcano_boxes.png -------------------------------------------------------------------------------- /images/volcano/volcano_boxes_ldl.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/images/volcano/volcano_boxes_ldl.png -------------------------------------------------------------------------------- /results/lpa_ldl_trigs.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/results/lpa_ldl_trigs.RData -------------------------------------------------------------------------------- /results/mr_ivw_phewas_clump2.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/results/mr_ivw_phewas_clump2.txt -------------------------------------------------------------------------------- /scripts/PheWAS.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/scripts/PheWAS.R -------------------------------------------------------------------------------- /scripts/figure_sensitivity_boxes.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/scripts/figure_sensitivity_boxes.R -------------------------------------------------------------------------------- /scripts/figure_volcano_plots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/scripts/figure_volcano_plots.R -------------------------------------------------------------------------------- /scripts/ldl-chd.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/scripts/ldl-chd.R -------------------------------------------------------------------------------- /scripts/pleiotropy_model_plots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/scripts/pleiotropy_model_plots.R -------------------------------------------------------------------------------- /scripts/run_mr.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/scripts/run_mr.R -------------------------------------------------------------------------------- /scripts/tables.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/scripts/tables.R -------------------------------------------------------------------------------- /tables/drug_prediction.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/tables/drug_prediction.csv -------------------------------------------------------------------------------- /tables/drug_proxy_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/tables/drug_proxy_results.csv -------------------------------------------------------------------------------- /tables/instruments.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/tables/instruments.csv -------------------------------------------------------------------------------- /tables/mr_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/tables/mr_results.csv -------------------------------------------------------------------------------- /tables/study.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/explodecomputer/mr-base-methods-paper/HEAD/tables/study.csv --------------------------------------------------------------------------------