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https://github.com/kenhanscombe/ukbtools
An R package to manipulate and explore UK Biobank data
https://github.com/kenhanscombe/ukbtools
biobank kcl-sgu r uk-biobank ukb
Last synced: about 9 hours ago
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An R package to manipulate and explore UK Biobank data
- Host: GitHub
- URL: https://github.com/kenhanscombe/ukbtools
- Owner: kenhanscombe
- Created: 2017-02-17T09:53:22.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2023-02-22T09:51:20.000Z (over 1 year ago)
- Last Synced: 2024-10-03T07:16:45.223Z (about 1 month ago)
- Topics: biobank, kcl-sgu, r, uk-biobank, ukb
- Language: HTML
- Homepage: https://kenhanscombe.github.io/ukbtools/
- Size: 11.2 MB
- Stars: 96
- Watchers: 9
- Forks: 26
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- awesome-uk-biobank - ukbtools
README
ukbtools 
===
[](https://cran.r-project.org/package=ukbtools)
[](https://codecov.io/gh/kenhanscombe/ukbtools)
[](https://github.com/kenhanscombe/ukbtools/actions)
> **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](http://www.ukbiobank.ac.uk/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
```r
# 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):
```bash
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](http://biobank.ctsu.ox.ac.uk/crystal/docs/UsingUKBData.pdf) 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.
```r
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
```r
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](https://kenhanscombe.github.io/ukbtools/) and in the package vignette "Explore UK Biobank Data"
```r
vignette("explore-ukb-data", package = "ukbtools")
```
For a list of all functions
```r
help(package = "ukbtools")
```