risk_factor {UKB.COVID19}

Generate covariate file

Description

This function formats and outputs a covariate table, used for input for other functions.

Usage

risk_factor(
  ukb.data,
  ABO.data = NULL,
  hesin.file,
  res.eng,
  res.wal = NULL,
  res.sco = NULL,
  fields = NULL,
  field.names = NULL
)

Arguments

ukb.data

tab delimited UK Biobank phenotype file. The file should include fields of gender, year of birth, BMI, ethnic background, SES, and smoking.

ABO.data

Latest yyyymmdd_covid19_misc.txt file.

hesin.file

Latest yyyymmdd_hesin.txt 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.

fields

User specified field codes from ukb.data file.

field.names

User specified field names.

Value

Outputs a covariate table, used for input for other functions. Automatically returns sex, age at birthday in 2020, SES, self-reported ethnicity, most recently reported BMI, most recently reported pack-years, whether they reside in aged care (based on hospital admissions data, and covid test data) and blood type. Function also allows user to specify fields of interest (field codes, provided by UK Biobank), and allows the users to specify more intuitive names, for selected fields.

Examples

## Not run: 
covars <- risk_factor(ukb.data=covid_example("sim_ukb.tab.gz"),
ABO.data=covid_example("sim_covid19_misc.txt.gz"),
hesin.file=covid_example("sim_hesin.txt.gz"),
res.eng=covid_example("sim_result_england.txt.gz"))

## End(Not run)