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Read UK Biobank codings file into lookup tables

Source: R/read_ukb_codings.R
read_ukb_codings.Rd

Reads the UK Biobank codings file (Codings.tsv) and returns lookup tables for OPCS-4 and UKB self-reported condition/medication/operation code types.

Usage

read_ukb_codings(
  path = get_ukb_codings(),
  tables = c("opcs4_lkp", "data_coding_3", "data_coding_4", "data_coding_5",
    "data_coding_6"),
  version = "v0",
  source = "https://biobank.ctsu.ox.ac.uk/crystal/exinfo.cgi?src=accessing_data_guide"
)

Arguments

path

Path to the Codings.tsv file. Default uses get_ukb_codings() to download the file.

tables

Character vector of table names to read. Available tables:

  • "opcs4_lkp" — OPCS-4 procedure lookup

  • "data_coding_3" — self-reported cancer (UKB field coding 3)

  • "data_coding_4" — self-reported medications (UKB field coding 4)

  • "data_coding_5" — self-reported operations (UKB field coding 5)

  • "data_coding_6" — self-reported non-cancer illnesses (UKB field coding 6)

By default, all five tables are returned.

version

Character string for the version label (default: "v0").

source

Character string for the data source URL or description.

Value

A named list where each element corresponds to a requested table, containing:

  • lookup: a list with table (data frame) and metadata (list)

See also

add_ukb_codings(), get_ukb_codings()

Examples

result <- read_ukb_codings(
  path = dummy_ukb_codings_path(),
  tables = "opcs4_lkp"
)
result$opcs4_lkp$lookup$table
#> # A tibble: 6 × 2
#>   opcs4_code description                                                   
#>   <chr>      <chr>                                                         
#> 1 H01        H01 Emergency excision of appendix                            
#> 2 H011       H01.1 Emergency excision of abnormal appendix and drainage HFQ
#> 3 H012       H01.2 Emergency excision of abnormal appendix NEC             
#> 4 H013       H01.3 Emergency excision of normal appendix                   
#> 5 H018       H01.8 Other specified emergency excision of appendix          
#> 6 H019       H01.9 Unspecified emergency excision of appendix