DOI: 10.5281/zenodo.17871008
title: Complete Regression Output Data Generated by OralMicroNHANES Survey‑Weighted Association Pipelines

description: Input data can be found in: Input Data for Replicating OralMicroNHANES Analyses.This dataset contains the full set of output files produced by OralMicroNHANES repository  after executing the following pipelines:



scripts/0_transform_n_preprocess_ssfiles

scripts/1_association_pipeline


These directories include all regression results, summaries, and intermediate objects generated during survey‑weighted microbiome association analyses. Each folder corresponds to one of the five Weighted Association Study (WAS) frameworks, reflecting the model specifications: 



Demographics → Microbiome (Linear)

Microbiome → Oral Conditions (Logistic)

Blood/Urine Exposure Markers → Microbiome (Linear)

Microbiome → Measurable Phenotypes (Linear)

Microbiome → Disease Incidents (Logistic)


Models use clr‑transformed genus‑level abundances or relative abundance terms Mi,m, with a 13‑variable covariate set (age, gender, race/ethnicity, education, nativity, poverty‑to‑income ratio). These association study results files are expected to be organized as followed: 

OralMicroNHANES/results/  ├── 0_ss_files/  │   ├── 1_demoWAS_clr_schema_structure.csv  │   ├── 1_demoWAS_none_schema_structure.csv  │   ├── 2_oradWAS_clr_schema_structure.csv  │   ├── 2_oradWAS_none_schema_structure.csv  │   ├── 3_exWAS_clr_schema_structure.csv  │   ├── 3_exWAS_none_schema_structure.csv  │   ├── 4_pheWAS_clr_schema_structure.csv  │   ├── 4_pheWAS_none_schema_structure.csv  │   ├── 5_outWAS_clr_schema_structure.csv  │   └── 5_outWAS_none_schema_structure.csv  │  ├── 1_demoWAS_out/  │   ├── result_clr/  │   │   ├── 1_demoWAS_clr_aggregation_summary.txt  │   │   ├── 1_demoWAS_clr_glanced_complete.rds  │   │   ├── 1_demoWAS_clr_rsq_complete.rds  │   │   ├── 1_demoWAS_clr_tidied_complete.rds  │   │   ├── RSV_genus1000_relative.rds  │   │   ├── RSV_genus1001_relative.rds  │   │   ├── RSV_genus1002_relative.rds  │   │   └── ... (1353 files)  │   └── result_none/  │       ├── 1_demoWAS_none_aggregation_summary.txt  │       ├── 1_demoWAS_none_glanced_complete.rds  │       ├── 1_demoWAS_none_rsq_complete.rds  │       ├── 1_demoWAS_none_tidied_complete.rds  │       ├── RSV_genus1000_relative.rds  │       ├── RSV_genus1001_relative.rds  │       ├── RSV_genus1002_relative.rds  │       └── ... (1353 files)  │  ├── 2_oradWAS_out/  │   ├── result_clr/  │   │   ├── 2_oradWAS_clr_aggregation_summary.txt  │   │   ├── 2_oradWAS_clr_glanced_complete.rds  │   │   ├── 2_oradWAS_clr_rsq_complete.rds  │   │   ├── 2_oradWAS_clr_tidied_complete.rds  │   │   ├── DENTURE_OHAROCDE.rds  │   │   ├── GUM_DISEASE_OHAROCGP.rds  │   │   ├── ORAL_HYGIENE_OHAROCOH.rds  │   │   └── ... (8 files)  │   └── result_none/  │       ├── 2_oradWAS_none_aggregation_summary.txt  │       ├── 2_oradWAS_none_glanced_complete.rds  │       ├── 2_oradWAS_none_rsq_complete.rds  │       ├── 2_oradWAS_none_tidied_complete.rds  │       ├── DENTURE_OHAROCDE.rds  │       ├── GUM_DISEASE_OHAROCGP.rds  │       ├── ORAL_HYGIENE_OHAROCOH.rds  │       └── ... (8 files)  │  ├── 3_exWAS_out/  │   ├── result_clr/  │   │   ├── 3_exWAS_clr_aggregation_summary.txt  │   │   ├── 3_exWAS_clr_glanced_complete.rds  │   │   ├── 3_exWAS_clr_rsq_complete.rds  │   │   ├── 3_exWAS_clr_tidied_complete.rds  │   │   ├── RSV_genus1000_relative.rds  │   │   ├── RSV_genus1001_relative.rds  │   │   ├── RSV_genus1002_relative.rds  │   │   └── ... (1353 files)  │   └── result_none/  │       ├── 3_exWAS_none_aggregation_summary.txt  │       ├── 3_exWAS_none_glanced_complete.rds  │       ├── 3_exWAS_none_rsq_complete.rds  │       ├── 3_exWAS_none_tidied_complete.rds  │       ├── RSV_genus1000_relative.rds  │       ├── RSV_genus1001_relative.rds  │       ├── RSV_genus1002_relative.rds  │       └── ... (1353 files)  │  ├── 4_pheWAS_out/  │   ├── result_clr/  │   │   ├── 4_pheWAS_clr_aggregation_summary.txt  │   │   ├── 4_pheWAS_clr_glanced_complete.rds  │   │   ├── 4_pheWAS_clr_rsq_complete.rds  │   │   ├── 4_pheWAS_clr_tidied_complete.rds  │   │   ├── BMXARMC.rds  │   │   ├── BMXARML.rds  │   │   ├── BMXBMI.rds  │   │   └── ... (137 files)  │   └── result_none/  │       ├── 4_pheWAS_none_aggregation_summary.txt  │       ├── 4_pheWAS_none_glanced_complete.rds  │       ├── 4_pheWAS_none_rsq_complete.rds  │       ├── 4_pheWAS_none_tidied_complete.rds  │       ├── BMXARMC.rds  │       ├── BMXARML.rds  │       ├── BMXBMI.rds  │       └── ... (137 files)  │  └── 5_outWAS_out/      ├── result_clr/      │   ├── 5_outWAS_clr_aggregation_summary.txt      │   ├── 5_outWAS_clr_glanced_complete.rds      │   ├── 5_outWAS_clr_rsq_complete.rds      │   ├── 5_outWAS_clr_tidied_complete.rds      │   ├── ANGINA.rds      │   ├── ASTHMA.rds      │   ├── BRONCHITIS.rds      │   └── ... (20 files)      └── result_none/          ├── 5_outWAS_none_aggregation_summary.txt          ├── 5_outWAS_none_glanced_complete.rds          ├── 5_outWAS_none_rsq_complete.rds          ├── 5_outWAS_none_tidied_complete.rds          ├── ANGINA.rds          ├── ASTHMA.rds          ├── BRONCHITIS.rds          └── ... (20 files)