makePhenotypes {UKB.COVID19}

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)