https://github.com/kenhanscombe/ukbkings

KCL Interface to UKB Project Data on Rosalind HPC cluster
https://github.com/kenhanscombe/ukbkings

kcl-sgu kings-college-london uk-biobank

Last synced: about 2 months ago
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KCL Interface to UKB Project Data on Rosalind HPC cluster

• Host: GitHub
• URL: https://github.com/kenhanscombe/ukbkings
• Owner: kenhanscombe
• License: other
• Created: 2019-12-04T16:22:15.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2023-04-22T15:53:58.000Z (over 1 year ago)
• Last Synced: 2024-08-29T15:44:44.965Z (4 months ago)
• Topics: kcl-sgu, kings-college-london, uk-biobank
• Language: R
• Homepage: https://kenhanscombe.github.io/ukbkings/
• Size: 73.8 MB
• Stars: 13
• Watchers: 4
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
ukbkings 

===

[![R build status](https://github.com/kenhanscombe/ukbkings/workflows/R-CMD-check/badge.svg)](https://github.com/kenhanscombe/ukbkings/actions)

[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)

[![codecov](https://codecov.io/gh/kenhanscombe/ukbkings/branch/master/graph/badge.svg?token=90dtoi0RvG)](https://codecov.io/gh/kenhanscombe/ukbkings)

**Important: This package is a KCL R interface to UKB data on Rosalind/CREATE.

It is only useful for UKB-approved KCL reasearchers and their

collaborators, with an account on the Rosalind/CREATE HPC cluster.**

## Overview

The ukbkings package includes functions to access UK Biobank (UKB)

project data on the Rosalind/CREATE High Performance Computing (HPC) cluster,

for UKB-approved King's College London (KCL) researchers and

collaborators. Access to data for a particular project is restricted to

named collaborators on the project.

## Installation

Install this development version from github with:

```r

devtools::install_github("kenhanscombe/ukbkings", dependencies = TRUE, force = TRUE)

```

Or, use the docker image to run R in a container with ukbkings and dependencies installed.

Explicitly mount your study folder from your user directly for data storage, and the UKB

data folder for access to UKB application data.

```bash

singularity run --bind /scratch/users//:/,//ukbiobank:/ukbiobank docker://onekenken/ukbkings:0.2.3

```

**Note**: On Rosalind you first need to load the singularity module with `module load apps/singularity/3.5.3`; on CREATE the singularity command is immediately available.

## Project data

Project-specific phenotype data and genetic link files (.fam, .sample,

.dat) are in project-specific folders. The structure of a

project directory setup for use with ukbkings is documented in the

project setup tool,

[ukbproject](https://github.com/kenhanscombe/ukbproject).

**Note. Any additional downloads (e.g. data baskets and associated

keys, data downloads from the UKB data portal) should be stored in the

subdirectory raw/. (Do not create further subdirectories within this

folder)**