View source: R/comorbidity_summary.R
comorbidity_summary | R Documentation |
summarise disease history records of each individual from the hospital inpatient diagnosis data.
comorbidity_summary( ukb.data, hesin.file, hesin_diag.file, primary = FALSE, ICD10.file, Date.start = NULL, Date.end = NULL )
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. |
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.
## 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)
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