comorbidity_summary {UKB.COVID19}

Create comorbidity summary file

Description

summarise disease history records of each individual from the hospital inpatient diagnosis data.

Usage

comorbidity_summary(
  ukb.data,
  hesin.file,
  hesin_diag.file,
  primary = FALSE,
  ICD10.file,
  Date.start = NULL,
  Date.end = NULL
)

Arguments

ukb.data

tab delimited UK Biobank phenotype file, containing sample qc fields (with default UKBiobank codes as column names)

hesin.file

Latest hospital inpatient master file.

hesin_diag.file

Latest hospital inpatient diagnosis file.

primary

TRUE: include primary diagnosis only; FALSE: include all diagnoses.

ICD10.file

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

Date.start

Date, dd/mm/yyyy, select the start date of hospital inpatient record period.

Date.end

Date, dd/mm/yyyy, select the end date of hospital inpatient record period.

Value

Outputs comorbidity summary table, named comorbidity_<Date.start>_<Date.end>.RData, including phenotype, non-genetic risk factors and all comorbidities, which will be used in the comorbidity association tests.

Examples

## Not run: 
comorb <- comorbidity_summary(ukb.data=covid_example("sim_ukb.tab.gz"),
hesin.file=covid_example("sim_hesin.txt.gz"), 
hesin_diag.file=covid_example("sim_hesin_diag.txt.gz"), 
ICD10.file=covid_example("ICD10.coding19.txt.gz"),
primary = FALSE,
Date.start = "16/03/2020")

## End(Not run)