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).
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")
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