For a list of diagnostic codes get the HES, GP, cancer registry, operations, and self-reported illness data, matching the provided codes.
Valid code vocabularies are:
- ICD10 (for `hesin`, `death_cause` and `cancer_registry` searches) - fuzzy matching
- ICD9 (for `hesin` searches) - fuzzy matching
- Read2 / CTV3 (for `gp_clinical`) - exact matches on first 5 characters
- OPCS3 / OPCS4 (for `hesin_oper`) - fuzzy matching
- ukb_cancer / ukb_noncancer (for self-reported illness at UK Biobank assessments - all available will be searched) - exact matches
This function relies on exported raw data files and thus does not need to be run in a Spark cluster. If the files are not in the default locations for the package you will need to specify the `file_paths` to exported tables. Recommend to run `export_tables()` once in your project to export the tables to the default paths for the package.
Arguments
- codes_df
A data frame. Contains two columns: `code` and `vocab_id` i.e., a list of diagnostic codes, and an indicator of the vocabulary (ICD10, Read2, CTV3, OPCS3, OPCS4, ukb_cancer, and ukb_noncancer are recognised). Other columns are ignored.
- file_paths
A data frame. Columns must be `object` and `path` containing paths to required files. Default assumes you have the tables exported in the RAP environment from ukbrapR::export_tables()
default=ukbrapR:::ukbrapr_paths- verbose
Logical. Be verbose,
default=FALSE
Value
Returns a list of data frames (the participant data for the requested diagnosis codes: `death_cause`, `hesin_diag`, `hesin_oper`, `gp_clinical`, `cancer_registry` and `selfrep_illness`. Also includes the original codes list)
Examples
# example diagnostic codes for CKD from GEMINI multimorbidity project
codes_df_ckd <- ukbrapR:::codes_df_ckd
head(codes_df_ckd)
# Get diagnosis data - returns list of data frames (one per source)
# -- Requires exported tables - see `export_tables()`
diagnosis_list <- get_diagnoses(codes_df_ckd)
# don't forget to save and upload data to RAP persistent storage!
save(diagnosis_list, "ukbrap.CKD.emr.20231114.RDat")
upload_to_rap(file="ukbrap.CKD.*", dir="")