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https://github.com/OxWearables/ukb_download_and_prep_template
This repository facilitates common data pre-processing steps when working with UK Biobank data.
https://github.com/OxWearables/ukb_download_and_prep_template
Last synced: 4 months ago
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This repository facilitates common data pre-processing steps when working with UK Biobank data.
- Host: GitHub
- URL: https://github.com/OxWearables/ukb_download_and_prep_template
- Owner: OxWearables
- License: other
- Created: 2020-07-01T15:18:00.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2022-12-23T08:06:44.000Z (over 1 year ago)
- Last Synced: 2024-01-17T01:09:42.434Z (6 months ago)
- Language: Python
- Homepage: https://ukb-download-and-prep-template.readthedocs.io/en/latest/
- Size: 11 MB
- Stars: 12
- Watchers: 7
- Forks: 3
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Lists
- awesome-uk-biobank - ukb_download_and_prep_template - processing steps when working with UK Biobank data | (Data processing / Optical coherence tomography and fundus)
README
# ukb_download_and_prep_template
**This repository is no longer maintained. As a group, our workflows for preprocessing UK Biobank data now use the [UK Biobank RAP](https://www.ukbiobank.ac.uk/enable-your-research/research-analysis-platform). For example, see a demo workflow [here](https://github.com/OxWearables/rap_wearables).**
**WARNING:** The history of this repository was altered on 2022-08-24. Ideally please delete any old copies you have of this repository and make a fresh clone. In particular, please do not submit pull requests using the old history.
**WARNING:** This template was written to work with data in formats provided directly by UK Biobank via the Showcase or Data Portal (traditional access route). It is unlikely to work correctly with data downloaded from the UKB RAP (new access route). For example, [this bug](https://github.com/OxWearables/ukb_download_and_prep_template/issues/10) has been reported. It should not be used with data downloaded from the RAP without suitable amendment.
**IMPORTANT**: If you used or are using a version of this repo from before 19.02.2021, an error in date processing may have caused wrongly assigned dates for health outcomes. Please re-download and re-process any data processed with `addNewHES.py`.
Detailed documentation is available [here](https://ukb-download-and-prep-template.readthedocs.io/).
*This was the in-development version and may require major changes and corrections - use at your own risk! Please share errors/bugs found, preferably directly on the GitHub page or by emailing [email protected]*.
## Quickstart
This usage tutorial assumes you have downloaded and extracted a `.csv` file containing participant data and a `hesin_all.csv` file with health record data from UK Biobank. The [download](https://github.com/activityMonitoring/ukb_download_and_prep_template/download) folder contains guidance on how to download these.
### 1. Installation
To use this repo, run:
```Bash
$ git clone https://github.com/activityMonitoring/ukb_download_and_prep_template.git
```
This repo requires `pandas` and `nltk`. If you are using an Anaconda installation of Python, these are included.
To install Anaconda, follow the instructions at https://docs.anaconda.com/anaconda/install/linux/.
Otherwise, run:
```Bash
$ pip install pandas
$ pip install nltk
```
Navigate to the repo:
```Bash
$ cd ukb_download_and_prep_template
```
### 2. Relabelling and recoding a participant data `.csv` file
You should have a `ukb12345.csv` participant data file which looks something like this:
| eid | 31-0.0 | 34-0.0 | 54-0.0 | ...
|---------|--------|--------|--------|--------
| 4987419 | 0 | 1944 | 11016 | ...
| 2898413 | 0 | 1956 | 11009 | ...
| 1049655 | 1 | 1947 | 11010 | ...
| 1892589 | 1 | 1941 | 11011 | ...
| 2449164 | 1 | 1958 | 11010 | ...
The next step towards having ready-to-use data is to filter out some columns and parse the field IDs and categorical codes.
#### Steps
1. Auto-generate a `columns.json` file from the text file of field IDs (in the format used in download_participant_data):
```Bash
$ python writeColumnsFile.py --columnsFile analysisCols.txt
```
2. Run:
```Bash
$ python filterUKB.py ukb12345.csv -o outputFilename.csv
```
### 3. Adding Hospital Episode Statistics on particular diseases
We now add columns on disease diagnoses in hospital.
You will need:
- `hesin_all.csv`: this is a file containing Hospital Episode Statistics data for all participants.
- `icdGroups.json`: this is a JSON file containing descriptions of required HES code.
- An existing dataset `input.csv` (which might be `outputFilename.csv` from the last section).
- If you want to define prevalent and incident disease, `input.csv` should also contain a date column which will be used to define this.
Then run:
```
$ python addNewHES.py input.csv hesin_all.csv output.csv icdGroups.json --incident_prevalent True --date_column 'name_of_date_column'
```