“None” means AHI <5
The reference group comprises referred adults with sleep studies and AHI below 5. It is not a population-level healthy control. Severe versus None is the default pairwise contrast.
Research guide
Methods & interpretation
How to read OSA associations across disease endpoints, adjustment models, statistical flags, and staged atlas releases.
Study frame
Cohort, reference, and time direction
Interpret every estimate within the sleep-clinic referral cohort.
Disease already present
L1-regularized logistic models summarize disease presence before index as odds ratios. Estimates are shrunk and intervals are non-classical; they should be labeled accordingly.
Disease arising during follow-up
Ridge cause-specific Cox models follow at-risk participants after index and report hazard ratios. At-risk counts, event counts, and proportional-hazards diagnostics belong with each result.
Odds ratios and hazard ratios answer different questions. They are shown in separate views and should not be compared as though they were the same estimand.
Incidence PheDAS survival analysis
Cumulative incidence, with death treated as competing
The curves describe absolute observed incidence; they are not M4-adjusted hazard ratios.
Aalen–Johansen curves
The curve view reports cumulative incidence from index through six years while treating death as a competing event. It does not use one minus Kaplan–Meier, which would overstate incidence when a competing event is present.
Post-selection description
Curves are available for the 40 PheCodes that were FDR-significant in at least one M4 OSA-severity contrast, including one visibly labeled OSA-recoding control. The curves describe those selected outcomes; they are not independent confirmation.
Descriptive, not a treatment effect
CPAP strata are observational and include only participants with recorded usage. Missing usage is not a no-CPAP group. Confounding, adherence selection, and exposure timing prevent causal treatment interpretation; No OSA is repeated as a common external reference.
Exact monthly at-risk and cumulative-event cells, uncertainty bands, and downloads are unavailable in this preview. Count arrays remain outside the browser bundle pending an institution-approved primary and complementary disclosure policy. Follow-up ends May 31, 2023, and late curve tails may be supported by thinner risk sets.
Explore cumulative incidence curves →PheDAS adjustment ladder
Read disease-model M1 through M4 as a sequence
ModelFramingInterpretationDisplay
M1CrudeUnadjusted association model.Comparison
M2DemographicsAdds demographic adjustment.Comparison
M3Extended · excludes BMIAdds family-specific adjustment while excluding BMI. Incidence PheDAS M3 also includes baseline encounter rate.Adjacent
M4Primary · adds BMIAdds BMI to M3. M3 remains adjacent because BMI may be treated as a confounder or as part of the pathway, depending on the scientific question.Primary
Model labels are family-specific. Other WAS views therefore retain neutral M1-M4 identifiers and do not assume that their covariate sets are interchangeable with PheDAS.
Statistical reading
Multiplicity, diagnostics, and uncertainty
Significance is context for an estimate, not a scientific conclusion.
Keep correction families intact
Current disease outputs expose FDR and Bonferroni significance flags. Exact adjusted q-values are not generally available. The atlas does not infer one global correction across incompatible analyses, models, or contrasts.
Warnings stay visible
Unstable estimates remain labeled rather than silently removed. Incidence results additionally expose event-per-variable warnings and proportional-hazards diagnostic information where available.
Association, not causation
Results support hypothesis generation. They do not establish causal, protective, or independent risk effects, and they do not estimate population OSA prevalence.
Other association families
Keep each clinical signal on its native scale
AnalysisEstimandInterpretation ruleDefault
LabWAS
β / OR / IRRMean and median value betas use rank-inverse-normal standard-deviation units and condition on being tested. Ordering propensity and ordering rate remain separate extensive and intensive signals.M4 · Severe vs NoneMedWAS
ORBinary ever-filled medication classes use zero-preserved GPI-4 codes. Fallback class labels remain visibly marked for review.M4 · Severe vs NoneBehWAS
OR or βBinary and rank-inverse-normal standardized continuous representations remain on separate axes. This small curated scan is preliminary and forest-first.M4 · Severe vs NoneProcWAS
IRRProcedure counts are annualized rates over one- and five-year pre-index windows; sleep-study and PAP-pathway procedures were excluded.M4 · Severe vs NoneUtilWAS
OR / IRRPresence and count among present are a two-part analysis. Physician and allied-health definitions must not be summed while their overlap rule remains under review.M4 · Severe vs NoneOmnibus rows are non-directional Wald statistics. They appear only in Manhattan and table views, never on a signed volcano or forest axis.
Release roadmap
Seven clinical lenses, released in stages
AnalysisScientific focusStatusRelease rule
Prevalence PheDASExisting disease · ORResearch previewDisease scan
Incidence PheDASNew-onset disease · HRResearch previewDisease scan
LabWASValues, ordering propensity, and ordering rateArchived snapshotVisible with snapshot or review warning
MedWASMedication fills · ORArchived snapshotVisible with snapshot or review warning
BehWASEHR-derived behaviors · OR or βPreliminary archivedVisible with snapshot or review warning
ProcWASProcedure rates · IRRArchived snapshotVisible with snapshot or review warning
UtilWASHealthcare-use presence and countsArchived reviewVisible with snapshot or review warning
Ready to explore?
Begin with the primary M4 Severe-versus-None view, then inspect M3 and the alternate contrasts before drawing a scientific conclusion.
Explore other WAS families →