Result tables description

Result of PheWAS analysis

Variable Name	Type	Description
phecode	String/Float	Phecode included in the PheWAS result
disease	String	Disease name corresponding to the phecode
system	String	Phecode disease system corresponding to the phecode
sex	String	Sex specificity of the phecode (Both, Male, or Female)
N_cases_exposed	Integer	Number of exposed individuals diagnosed with the phecode during follow-up
describe	String	Model-fitting note or reason a full model estimate was not returned
exposed_group	String	Event summary for the exposed group, formatted as cases/person-years (incidence per 1,000 person-years)
unexposed_group	String	Event summary for the unexposed group, formatted as cases/person-years (incidence per 1,000 person-years)
phewas_coef	Float	Estimated effect size from the PheWAS model
phewas_se	Float	Standard error of the estimated effect size
phewas_p	Float	P-value from the PheWAS model
phewas_p_significance	Boolean	Whether the phecode is significant after multiple-testing correction
phewas_p_adjusted	Float	Adjusted P-value for phewas_p

For exposed-only cohort, the returned table is simpler: significance is based on the case-count threshold, and model-based columns such as phewas_coef, phewas_se, phewas_p, and phewas_p_adjusted may be absent.

Result of comorbidity strength estimation

Variable Name	Type	Description
phecode_d1	Float	Phecode for disease 1 in the disease pair
phecode_d2	Float	Phecode for disease 2 in the disease pair
name_disease_pair	String	Disease-pair label in the format D1-D2
N_exposed	Integer	Total number of exposed individuals in the analysis dataset
n_total	Integer	Number of exposed individuals eligible for the pair-specific analysis after excluding ineligible disease histories
n_d1d2_diagnosis	Integer	Number of eligible individuals diagnosed with both diseases
n_d1_diagnosis	Integer	Number of eligible individuals diagnosed with disease 1
n_d2_diagnosis	Integer	Number of eligible individuals diagnosed with disease 2
n_d1d2_nontemporal	Integer	Number of individuals with a non-temporal D1-D2 pair
n_d1d2_temporal	Integer	Number of individuals with temporal order D1 -> D2
n_d2d1_temporal	Integer	Number of individuals with temporal order D2 -> D1
n_d1d2_pair	Integer	Total number of individuals contributing a D1/D2 pair, counting temporal and non-temporal pair occurrences together
description	String	Note describing why statistics were not estimated, if applicable
phi	Float	Phi correlation for the disease pair
phi_theta	Float	Standard-error term used for inference on phi
phi_p	Float	P-value for phi correlation
RR	Float	Relative risk for co-occurrence of the disease pair
RR_theta	Float	Standard-error term used for inference on RR
RR_p	Float	P-value for relative risk
phi_p_significance	Boolean	Whether phi_p is significant after correction
phi_p_adjusted	Float	Adjusted P-value for phi_p
RR_p_significance	Boolean	Whether RR_p is significant after correction
RR_p_adjusted	Float	Adjusted P-value for RR_p
disease_d1	String	Disease name for phecode_d1
system_d1	String	Disease system for phecode_d1
sex_d1	String	Sex specificity for phecode_d1
disease_d2	String	Disease name for phecode_d2
system_d2	String	Disease system for phecode_d2
sex_d2	String	Sex specificity for phecode_d2

Result of binomial test

Variable Name	Type	Description
phecode_d1	Float	Phecode for disease 1 in the temporal disease pair
phecode_d2	Float	Phecode for disease 2 in the temporal disease pair
name_disease_pair	String	Temporal disease-pair label, typically D1->D2
n_d1d2_nontemporal	Integer	Number of individuals with a non-temporal D1-D2 pair
n_d1d2_temporal	Integer	Number of individuals with temporal order D1 -> D2
n_d2d1_temporal	Integer	Number of individuals with temporal order D2 -> D1
binomial_p	Float	P-value from the binomial test for directionality
binomial_proportion	Float	Estimated directionality proportion from the binomial test
binomial_proportion_ci	String	Confidence interval for the directionality proportion
binomial_p_significance	Boolean	Whether binomial_p is significant after correction
binomial_p_adjusted	Float	Adjusted P-value for binomial_p
disease_d1	String	Disease name for phecode_d1
system_d1	String	Disease system for phecode_d1
sex_d1	String	Sex specificity for phecode_d1
disease_d2	String	Disease name for phecode_d2
system_d2	String	Disease system for phecode_d2
sex_d2	String	Sex specificity for phecode_d2

Result of comorbidity network analysis

Variable Name	Type	Description
phecode_d1	Float	Phecode for disease 1 in the non-temporal disease pair
phecode_d2	Float	Phecode for disease 2 in the non-temporal disease pair
name_disease_pair	String	Disease-pair label in the format D1-D2
N_exposed	Integer	Total number of exposed individuals in the analysis dataset
n_total	Integer	Number of individuals included in the pair-specific regression analysis
n_exposed/n_cases	String	Exposure summary among cases for the pair-specific model
n_exposed/n_controls	String	Exposure summary among controls for the pair-specific model
comorbidity_network_method	String	Method used for comorbidity network analysis (CN, RPCN, or PCN_PCA)
describe	String	Model-fitting description, including removed covariates when relevant
co_vars_list	String	Covariates retained in the fitted model
co_vars_zvalues	String	Z-values for covariates retained in the fitted model
comorbidity_beta	Float	Estimated effect size from the comorbidity network model
comorbidity_se	Float	Standard error of the estimated effect size
comorbidity_p	Float	P-value for the comorbidity network effect
comorbidity_aic	Float	Akaike information criterion of the fitted model
comorbidity_p_significance	Boolean	Whether comorbidity_p is significant after correction
comorbidity_p_adjusted	Float	Adjusted P-value for comorbidity_p
disease_d1	String	Disease name for phecode_d1
system_d1	String	Disease system for phecode_d1
sex_d1	String	Sex specificity for phecode_d1
disease_d2	String	Disease name for phecode_d2
system_d2	String	Disease system for phecode_d2
sex_d2	String	Sex specificity for phecode_d2

Method-specific columns

Variable Name	Type	Description
alpha	Float	Present for RPCN; the L1 penalty level used in the final model
pc_sum_variance_explained	Float	Present for PCN_PCA; cumulative variance explained by retained principal components

Result of disease trajectory analysis

Variable Name	Type	Description
phecode_d1	Float	Phecode for disease 1 in the temporal disease pair
phecode_d2	Float	Phecode for disease 2 in the temporal disease pair
name_disease_pair	String	Temporal disease-pair label, typically D1->D2
N_exposed	Integer	Total number of exposed individuals in the analysis dataset
n_total	Integer	Number of individuals included in the nested case-control analysis for the pair
n_exposed/n_cases	String	Exposure summary among sampled cases
n_exposed/n_controls	String	Exposure summary among sampled controls
trajectory_method	String	Method used for disease trajectory analysis (CN, RPCN, or PCN_PCA)
describe	String	Model-fitting description, including removed covariates when relevant
co_vars_list	String	Covariates retained in the fitted model
co_vars_zvalues	String	Z-values for covariates retained in the fitted model
trajectory_beta	Float	Estimated effect size from the trajectory model
trajectory_se	Float	Standard error of the estimated effect size
trajectory_p	Float	P-value for the trajectory effect
trajectory_aic	Float	Akaike information criterion of the fitted model
trajectory_p_significance	Boolean	Whether trajectory_p is significant after correction
trajectory_p_adjusted	Float	Adjusted P-value for trajectory_p
disease_d1	String	Disease name for phecode_d1
system_d1	String	Disease system for phecode_d1
sex_d1	String	Sex specificity for phecode_d1
disease_d2	String	Disease name for phecode_d2
system_d2	String	Disease system for phecode_d2
sex_d2	String	Sex specificity for phecode_d2

Method-specific columns

Variable Name	Type	Description
alpha	Float	Present for RPCN; the L1 penalty level used in the final model
pc_sum_variance_explained	Float	Present for PCN_PCA; cumulative variance explained by retained principal components