map_clinical_events_to_phecodes: Map UK Biobank clinical events to phecodes

In rmgpanw/codemapper: Functions for Mapping Between Clinical Coding Systems

Map UK Biobank clinical events to phecodes

Description

UK Biobank clinical events sources that are recorded in ICD10 are mapped directly to phecodes, while non-ICD10 sources are mapped to phecodes via ICD10.

Usage

map_clinical_events_to_phecodes(
  clinical_events,
  all_lkps_maps = NULL,
  min_date_only = FALSE,
  col_filters = default_col_filters()
)

Arguments

clinical_events	A long format data frame created by tidy_clinical_events, tidy_gp_clinical, tidy_gp_scripts or make_clinical_events_db. This can also be a tbl_dbi object.
all_lkps_maps	Either a named list of lookup and mapping tables (either data frames or tbl_dbi objects), or the path to a SQLite database containing these tables (see also build_all_lkps_maps() and all_lkps_maps_to_db()). If NULL, will attempt to connect to an SQLite database named 'all_lkps_maps.db' in the current working directory, or to a a SQLite database specified by an environmental variable named 'ALL_LKPS_MAPS_DB' (see here for how to set environment variables using a .Renviron file). The latter method will be used in preference.
min_date_only	If TRUE, result will be filtered for only the earliest date per eid-phecode pair (date will be recorded as NA for cases where there are no dates).
col_filters	A named list where each name in the list refers to the name of a lookup or mapping table. Each item is also a named list, where the names refer to column names in the corresponding table, and the items are vectors of values to filter for. For example, ⁠list(my_lookup_table = list(colA = c("A", "B"))⁠ will result in my_lookup_table being filtered for rows where colA is either 'A' or 'B'. Uses default_col_filters() by default. Set to NULL to remove all filters.

Details

Maps the following UK Biobank clinical events sources to phecodes: f40001, f40002, f20002_icd10, f40006, f41270, f40013, f41271, gpc1_r3, gpc2_r3, gpc3_r3, gpc4_r3, gpc1_r2, gpc2_r2, gpc3_r2, gpc4_r2.

Value

A data frame with column names 'eid', 'source', 'index', 'code', 'icd10', 'phecode' and 'date'.

Examples

# build dummy all_lkps_maps
all_lkps_maps_dummy <- build_all_lkps_maps_dummy()

# dummy clinical events data frame
dummy_clinical_events_tidy()

# map to phecodes
map_clinical_events_to_phecodes(
  clinical_events = dummy_clinical_events_tidy(),
  all_lkps_maps = all_lkps_maps_dummy,
  min_date_only = FALSE
)

rmgpanw/codemapper documentation built on Aug. 30, 2023, 4:07 p.m.