makePhenotypes: Generate COVID-19 phenotypes

In UKB.COVID19: UK Biobank COVID-19 Data Processing and Risk Factor Association Tests

Generate COVID-19 phenotypes

Description

Generate COVID-19 phenotypes

Usage

makePhenotypes(
  ukb.data,
  res.eng,
  res.wal = NULL,
  res.sco = NULL,
  death.file,
  death.cause.file,
  hesin.file,
  hesin_diag.file,
  hesin_oper.file,
  hesin_critical.file,
  code.file,
  pheno.type = "severity",
  Date = NULL
)

Arguments

ukb.data	tab delimited UK Biobank phenotype file.
res.eng	Latest covid result file/files for England.
res.wal	Latest covid result file/files for Wales. Only available for downloads after April 2021.
res.sco	Latest covid result file/files for Scotland. Only available for downloads after April 2021.
death.file	Latest death register file.
death.cause.file	Latest death cause file.
hesin.file	Latest hospital inpatient master file.
hesin_diag.file	Latest hospital inpatient diagnosis file.
hesin_oper.file	Latest hospital inpatient operation file.
hesin_critical.file	Latest hospital inpatient critical care file.
code.file	The operation code file, which is included in the package.
pheno.type	The phenotype options, which include "susceptibility", "severity", and "mortality".
Date	Date, ddmmyyyy, select the results until a certain date. By default, Date = NULL, the latest hospitalization date.

Value

Returns a data.frame with phenotypes for COVID-19 susceptibility, severity and mortality.

Examples

## Not run: 
pheno <- makePhenotypes(ukb.data=covid_example("sim_ukb.tab.gz"),
res.eng=covid_example("sim_result_england.txt.gz"),
death.file=covid_example("sim_death.txt.gz"),
death.cause.file=covid_example("sim_death_cause.txt.gz"),
hesin.file=covid_example("sim_hesin.txt.gz"),
hesin_diag.file=covid_example("sim_hesin_diag.txt.gz"),
hesin_oper.file=covid_example("sim_hesin_oper.txt.gz"),
hesin_critical.file=covid_example("sim_hesin_critical.txt.gz"),
code.file=covid_example("coding240.txt.gz"),
pheno.type = "severity")

## End(Not run)

UKB.COVID19 documentation built on March 18, 2022, 8:03 p.m.