Complete Regression Output Data Generated by OralMicroNHANES Survey‑Weighted Association Pipelines

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)可从《用于复现OralMicroNHANES分析的输入数据集》（Input Data for Replicating OralMicroNHANES Analyses）获取本数据集的源输入数据。本数据集包含OralMicroNHANES代码库执行以下分析流程后生成的全部输出文件： scripts/0_transform_n_preprocess_ssfiles scripts/1_association_pipeline 上述目录包含调查加权微生物组关联分析过程中产生的所有回归分析结果、汇总文件与中间产出对象。每个子目录对应5种加权关联研究（Weighted Association Study, WAS）框架之一，对应模型设定如下： 1. 人口统计学特征→微生物组（线性模型） 2. 微生物组→口腔疾病状况（逻辑回归模型） 3. 血液/尿液暴露标志物→微生物组（线性模型） 4. 微生物组→可测量表型（线性模型） 5. 微生物组→疾病发病情况（逻辑回归模型） 本次分析采用中心化对数比（centered log-ratio, clr）变换后的属水平丰度或相对丰度项$M_{i,m}$，并使用包含13个变量的协变量集：年龄、性别、种族/族裔、教育水平、出生地、贫困收入比。本关联分析结果文件的组织形式如下： 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)