Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/machiela-lab/UKBBcleanR
Prepare electronic medical record data from the UK Biobank for time-to-event analyses
https://github.com/machiela-lab/UKBBcleanR
data-processing electronic-medical-records r r-package rstats rstats-package time-to-event uk-biobank
Last synced: 2 days ago
JSON representation
Prepare electronic medical record data from the UK Biobank for time-to-event analyses
- Host: GitHub
- URL: https://github.com/machiela-lab/UKBBcleanR
- Owner: machiela-lab
- License: mit
- Created: 2022-08-02T23:56:25.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2023-01-26T14:53:31.000Z (almost 2 years ago)
- Last Synced: 2024-08-02T16:47:10.550Z (3 months ago)
- Topics: data-processing, electronic-medical-records, r, r-package, rstats, rstats-package, time-to-event, uk-biobank
- Language: R
- Homepage:
- Size: 1.23 MB
- Stars: 10
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-uk-biobank - UKBBcleanR - to-event analyses | (Data processing / Optical coherence tomography and fundus)
README
UKBBcleanR: Prepare electronic medical record data from the UK Biobank for time-to-event analyses 
===================================================
[](https://github.com/machiela-lab/UKBBcleanR/actions/workflows/R-CMD-check.yaml)
[](https://opensource.org/licenses/MIT)
[](https://doi.org/10.5281/zenodo.7301712)
**Date repository last updated**: January 26, 2023
### Overview
The `UKBBcleanR` package contains an `R` function that prepares time-to-event data from raw [UK Biobank](https://www.ukbiobank.ac.uk/) electronic medical record data. The prepared data can be used for cancer outcomes, but could be modified for other health outcomes. This package is not available on [CRAN](https://cran.r-project.org/).
### Installation
To install the development version from GitHub:
devtools::install_github("machiela-lab/UKBBcleanR")
### Available function(s)
Function
Description
tte
Prepares time-to-event data from raw UK Biobank electronic medical record data.
The repository also includes the resources and code to create the project hex sticker.
### Authors
* **Alexander Depaulis** - *Integrative Tumor Epidemiology Branch (ITEB), Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, Maryland (MD), USA* - [GitHub](https://github.com/adepaulis1)
* **Derek W. Brown** - *ITEB, DCEG, NCI, NIH, Rockville, MD, USA (original)* - [GitHub](https://github.com/derekbrown12) - [ORCID](https://orcid.org/0000-0001-8393-1713)
* **Aubrey K. Hubbard** - *ITEB, DCEG, NCI, NIH, Rockville, MD, USA* - [ORCID](https://orcid.org/0000-0003-4052-1110)
See also the list of [contributors](https://github.com/machiela-lab/UKBBcleanR/graphs/contributors) who participated in this package, including:
* **Ian D. Buller** - *Social & Scientific Systems, Inc., a division of DLH Corporation, Silver Spring, Maryland (current)* - *Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland (original)* - [GitHub](https://github.com/idblr) - [ORCID](https://orcid.org/0000-0001-9477-8582)
* **Mitchell J. Machiela** - *ITEB, DCEG, NCI, NIH, Rockville, MD, USA* - [GitHub](https://github.com/machiela) - [ORCID](https://orcid.org/0000-0001-6538-9705)
### Getting Started
The `tte` function requires several raw [UK Biobank](https://www.ukbiobank.ac.uk/) variables to run correctly. A detailed list of required variables are provided in the [README_required_variables.txt](https://github.com/machiela-lab/UKBBcleanR/blob/main/data-raw/README_required_variables.txt) file.
Data can be loaded in the `tte` function in two ways:
* The user can specify a working directory using `setwd()` to where each individual data set is stored.
+ NOTE: These individual data sets must contain the specific variables and have names which match the [README_required_variables.txt](https://github.com/machiela-lab/UKBBcleanR/blob/main/data-raw/README_required_variables.txt) file. Example data is available within the [package](https://github.com/machiela-lab/UKBBcleanR/tree/main/inst/extdata).
* The user can generate a single data set containing all the variables of interest. This data set can then be loaded into the `tte` function using the `combined_data` argument. Example data is available within the [package](https://github.com/machiela-lab/UKBBcleanR/tree/main/inst/extdata).
### Usage
``` r
# ------------------ #
# Necessary packages #
# ------------------ #
library(UKBBcleanR)
# -------- #
# Settings #
# -------- #
##### Input UKBBcleanR sample data
# Use combined data set
testdata <- as.data.frame(combined_data)
# Set ICD-10 outcome of interest
cancer_outcome <- c("C911")
# Set prevalent cancers to identify in data cleaning
prevalent_cancers <- c("D37", "D38", "D39", "D40", "D41", "D42",
"D43", "D44", "D45", "D46", "D47", "D48")
# Set incident cancers to identify in data cleaning
incident_cancers <- c("C900")
# ------- #
# Run tte #
# ------- #
# Run without removing prevalent cancers from analysis
test1 <- tte(combined_data = testdata,
cancer_of_interest_ICD10 = cancer_outcome,
prevalent_cancer_list = prevalent_cancers,
prevalent_C_cancers = TRUE,
incident_cancer_list = incident_cancers,
remove_prevalent_cancer = FALSE,
remove_self_reported_cancer = FALSE)
table(test1$case_control_cancer_ignore) # tte outcome ignoring other incident cancers
table(test1$case_control_cancer_control) # tte outcome controlling for other incident cancers
# Run with removing prevalent cancers from analysis
test2 <- tte(combined_data = testdata,
cancer_of_interest_ICD10 = cancer_outcome,
prevalent_cancer_list = prevalent_cancers,
prevalent_C_cancers = TRUE,
incident_cancer_list = incident_cancers,
remove_prevalent_cancer = TRUE,
remove_self_reported_cancer = TRUE)
table(test2$case_control_cancer_ignore) # tte outcome ignoring other incident cancers
table(test2$case_control_cancer_control) # tte outcome controlling for other incident cancers
```
### Vignette
We provide a [vignette](https://htmlpreview.github.io/?https://github.com/machiela-lab/UKBBcleanR/blob/main/vignettes/vignette.html) with a practical example and work through of the provided [example data](https://github.com/machiela-lab/UKBBcleanR/tree/main/inst/extdata).
### Funding
Package was developed while the first author was a participant of the 2022 [National Institutes of Health](https://www.nih.gov/) [Summer Internship Program in Biomedical Research](https://www.training.nih.gov/programs/sip) and while the second author was a postdoctoral fellow supported by the [Cancer Prevention Fellowship Program](https://cpfp.cancer.gov/) at the [National Cancer Institute](https://www.cancer.gov/) (NCI) and the third author was a postdoctoral fellow in the NCI [Division of Cancer Epidemiology and Genetics](https://dceg.cancer.gov/).
### Acknowledgments
When citing this package for publication, please cite follow:
citation("UKBBcleanR")
### Questions? Feedback?
For questions about the package please contact the maintainer [Dr. Derek Brown](mailto:[email protected]) or [submit a new issue](https://github.com/machiela-lab/UKBBcleanR/issues).