ukbtools

NB. With the advent of the UKB RAP, this package is no longer supported or under active development.

After downloading and decrypting your UK Biobank (UKB) data with the supplied [UKB programs] (http://biobank.ctsu.ox.ac.uk/crystal/docs/UsingUKBData.pdf), 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.

Installation

# Install from CRAN
install.packages("ukbtools")

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

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 ukbxxxx.tab 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.

library(ukbtools)
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")