extract_phenotypes: Extract phenotypes from clinical events data

In rmgpanw/ukbwranglr: Exploring UKB Data

Extract phenotypes from clinical events data

Description

Filters a clinical events table created by tidy_clinical_events for a set clinical codes that represent one or more phenotypes.

Usage

extract_phenotypes(
  clinical_events,
  clinical_codes,
  source_filter = NULL,
  verbose = TRUE
)

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.
clinical_codes	data frame. Must match the format as per example_clinical_codes.
source_filter	Character vector of data sources to filter for (optional).
verbose	If TRUE (default), display progress messages.

Value

A data frame.

See Also

Other clinical events: clinical_events_sources(), example_clinical_codes(), make_clinical_events_db(), tidy_clinical_events()

Examples

library(magrittr)

# dummy clinical events data frame
dummy_ukb_data_dict <- get_ukb_dummy("dummy_Data_Dictionary_Showcase.tsv")
dummy_ukb_codings <- get_ukb_dummy("dummy_Codings.tsv")

dummy_clinical_events <- read_ukb(
  path = get_ukb_dummy("dummy_ukb_main.tsv", path_only = TRUE),
  ukb_data_dict = dummy_ukb_data_dict,
  ukb_codings = dummy_ukb_codings
) %>%
  tidy_clinical_events(
    ukb_data_dict = dummy_ukb_data_dict,
    ukb_codings = dummy_ukb_codings
  ) %>%
  dplyr::bind_rows()

head(dummy_clinical_events)

# dummy clinical code list
example_clinical_codes()

# Filter for participants with matching clinical codes
extract_phenotypes(
  clinical_events = dummy_clinical_events,
  clinical_codes = example_clinical_codes()
)

rmgpanw/ukbwranglr documentation built on April 30, 2024, 7:47 a.m.