Manipulate and Explore UK Biobank Data

A set of tools to create a UK Biobank <> dataset from a UKB fileset (.tab, .r, .html), visualize primary demographic data for a sample subset, query ICD diagnoses, retrieve genetic metadata, read and write standard file formats for genetic analyses.

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Citing ukbtools

If you use ukbtools in any published work, please cite:

Hanscombe K.B., Coleman J.R.I., Traylor M., and Lewis C.M. ukbtools: An R package to manage and query UK Biobank data. bioRxiv 158113; doi:


After downloading and decrypting your UK Biobank (UKB) data with the supplied UKB programs, you have multiple files that need to be brought together to give you a dataset to explore. The data file has column names that are edited field-codes from the UKB data showcase. ukbtools makes it easy to collapse the multiple UKB files into a single dataset for analysis, in the process giving meaningful names to the variables. The package also includes functionality to retrieve ICD diagnoses, explore a sample subset in the context of the UKB sample, and collect genetic metadata.


# Install from CRAN
# Install latest development version
devtools::install_github("kenhanscombe/ukbtools", dependencies = TRUE)

Note: This package is in beta - it is feature complete but may contain unknown bugs. If anything does not work, first re-install the package devtools::install_github("kenhanscombe/ukbtools", dependencies = TRUE, force = TRUE) to get the latest development version. If it is still not working, let me know and I'll fix it.

Prerequisite: Make a UKB fileset

Download§ then decrypt your data and create a "UKB fileset" (.tab, .r, .html):

ukb_unpack ukbxxxx.enc key
ukb_conv ukbxxxx.enc_ukb r
ukb_conv ukbxxxx.enc_ukb docs

ukb_unpack decrypts your downloaded ukbxxxx.enc file, outputting a ukbxxxx.enc_ukb file. ukb_conv with the r flag converts the decrypted data to a tab-delimited file and an R script ukbxxxx.r that reads the tab file. The docs flag creates an html file containing a field-code-to-description table (among others).

§ Full details of the data download and decrypt process are given in the Using UK Biobank Data documentation.

Make a UKB dataset

The function ukb_df() takes two arguments, the stem of your fileset and the path, and returns a dataframe with usable column names. This will take a few minutes. The rate-limiting step is reading and parsing the code in the UKB-generated .r file - not ukb_df per se.

my_ukb_data <- ukb_df("ukbxxxx")

You can also specify the path to your fileset if it is not in the current directory. For example, if your fileset is in a subdirectory of the working directory called data

my_ukb_data <- ukb_df("ukbxxxx", path = "/full/path/to/my/data")

Note: You can move the three files in your fileset after creating them with ukb_conv, but they should be kept together. ukb_df() automatically updates the read call in the R source file to point to the correct directory (the current directory by default, or a directory specified by path).

Other tools

All tools are described on the ukbtools webpage and in the package vignette "Explore UK Biobank Data"

vignette("explore-ukb-data", package = "ukbtools")

For a list of all functions

help(package = "ukbtools")


ukbtools 0.11.0

Development version

Updated functionality:

  • ukb_df: Replaced readr::read_tsv with data.table::fread for faster read. Also includes an n_threads argument passed to data.table::fread, which may make read faster. Column names now include field code to ensure names are unique (UK Biobank sometimes use the same description for more than one variable)

Defunct functionality:

  • Added defunct message to ukb_gen_meta, ukb_gen_pcs, ukb_gen_excl, ukb_gen_rel, ukb_gen_het, ukb_gen_excl_to_na, and ukb_gen_write_plink_excl. ukb_defunct explains why these have become defunct and where to get UK Biobank genetic (meta)data.

New functionality:

  • Since the UKB changed the way they serve up genetic metadata, the following work with files described in UKB Resource 531: ukb_gen_sqc_names supplies column names for the separately downloaded sample QC file; ukb_gen_rel_count does the same as before (a count of levels of relatedness or a plot) but with separately downloaded relatedness data; ukb_gen_related_with_data returns subset of relatedness data in which both IDs have data on a phenotype of interest; ukb_gen_samples_to_remove returns a list of individuals to exclude in order to remove relatedness (one possible solution to a maximal subset problem).

ukbtools 0.10.1

Bug fix:

  • ukb_icd_freq_by: corrected order by levels of reference.var in the optional plot. (order in the default dataframe returned was correct.)

  • ukb_df: corrected tab file path update in r source file. Specifically, made regular expression more specific (1 case reported of regular expression matching word elsewhere in the source file.). Also, replaced utils::read.delim with readr::read_tsv for faster read, with progress bar.

ukbtools 0.10.0

New functionality:

  • ukb_icd_freq_by returns frequency for one or more ICD diagnoses by levels of a reference variable and includes an optional plot

  • ukb_df_full_join (a thin wrapper around dplyr::full_join) recursively called on a list of UKB datasets

  • ukb_df_duplicated_names to identify duplicated names within a dataset. The variable prefix (constructed from its description), index, and array should make the column name unique. However, typos in UKB documentation that give two variables the do not increment index/array have been observed. You will want to identify these and update them appropriately. We expect the occurrence of such duplicates will be rare.

Updated functionality:

  • ukb_icd_diagnosis now takes one or more individual ids and returns a dataframe with a potential message noting ids with no diagnoses

  • ukb_icd_keyword accepts a character vector of one or more "keywords" and returns all ICD descriptions including any of the keywords

ukbtools 0.9.0

  • beta release to CRAN. Feature complete but may contain unknown bugs.

Reference manual

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0.11.0 by Ken Hanscombe, 9 months ago

Browse source code at

Authors: Ken Hanscombe [aut, cre]

Documentation:   PDF Manual  

GPL-2 license

Imports dplyr, purrr, readr, ggplot2, XML, magrittr, grid, plyr, tibble, tidyr, scales, stringr, data.table

Suggests knitr, rmarkdown

See at CRAN