ukbtools: An R package to manage and query UK Biobank data
Ken B Hanscombe, Jonathan R I Coleman, Matthew Traylor, Cathryn M Lewis
bioRxiv 158113; doi: https://doi.org/10.1101/158113
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.
# Install from CRAN
install.packages("ukbtools")
# Install latest development version
devtools::install_github("kenhanscombe/ukbtools", build_vignettes = TRUE, 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", build_vignettes = TRUE, dependencies = TRUE, force = TRUE) to get the latest development version. If it is still not working, let me know and I'll fix it.
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.
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 in the package are described in the vignette "Explore UK Biobank Data"
vignette("explore-ukb-data", package = "ukbtools")
For a list of all functions
help(package = "ukbtools")