comorbidity_asso {UKB.COVID19}

Generate comorbidity association result file

Description

Association tests between each co-morbidity and given phenotype (susceptibility, mortality or severity) with the adjustment of covariates.

Usage

comorbidity_asso(
  pheno,
  covariates,
  cormorbidity,
  population = "all",
  cov.name = c("sex", "age", "bmi"),
  phe.name,
  ICD10.file
)

Arguments

pheno

phenotype dataframe - output from makePheno function

covariates

covariate dataframe - output from risk.factor function. Optional.

cormorbidity

Comorbidity summary generated from comorbidity.summary.

population

Choose self-report population/ethnic background group from "all", white", "black", "asian", "mixed", or "other". By default, population="all", include all ethnic groups.

cov.name

Selected covariates names. By default, cov.name=c("sex","age","bmi"), covariates are sex age and BMI.

phe.name

Phenotype name.

ICD10.file

The ICD10 code file, which is included in the package.

Value

Outputs a comorbidity association test result with OR, 95% CI and p-value.

Examples

## Not run: 
comorb.asso <- comorbidity_asso(pheno=phe,
covariates=covar,
cormorbidity=comorb,
population="white",
cov.name=c("sex","age","bmi","SES","smoke","inAgedCare"),
phe.name="hospitalisation",
ICD10.file=covid_example("ICD10.coding19.txt.gz"))

## End(Not run)