penprs

Penalized Regression for Inference of Polygenic Risk Scores

https://github.com/shz9/penprs

Science Score: 67.0%

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Links to: medrxiv.org
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Low similarity (7.8%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Penalized Regression for Inference of Polygenic Risk Scores

Basic Info

Host: GitHub
Owner: shz9
License: mit
Language: Python
Default Branch: main
Size: 72.3 KB

Statistics

Stars: 1
Watchers: 2
Forks: 2
Open Issues: 0
Releases: 0

Created about 1 year ago · Last pushed 7 months ago

Metadata Files

Readme Changelog License Citation

PenPRS: Penalized Regression for Inference of Polygenic Risk Scores

:hammer: Under Construction :construction:

``` -->-->-->-->->->->->-------<-<-<--<-<--<-<--<--

▗▄▄▖  ▗▄▄▄▖ ▗▖  ▗▖ ▗▄▄▖  ▗▄▄▖   ▗▄▄▖
▐▌ ▐▌ ▐▌    ▐▛▚▖▐▌ ▐▌ ▐▌ ▐▌ ▐▌ ▐▌
▐▛▀▘  ▐▛▀▀▘ ▐▌ ▝▜▌ ▐▛▀▘  ▐▛▀▚▖  ▝▀▚▖
▐▌    ▐▙▄▄▖ ▐▌  ▐▌ ▐▌    ▐▌ ▐▌ ▗▄▄▞▘

Penalized Regression for Polygenic Risk Scores Version: 0.0.1 | Release date: January 2025 Authors: Shadi Zabad & Jack Song McGill University -->-->-->-->->->->->-------<-<-<--<-<--<-<--<-- ```

Installation

To install the package from GitHub, use the following command:

bash pip install git+https://github.com/shz9/penprs.git

Usage

```python import magenpy as mgp from penprs.model.Lasso import Lasso

Load the data

gdl = mgp.GWADataLoader(mgp.tgpeurdatapath(), sumstatsfiles=mgp.ukbheightsumstatspath(), sumstatsformat="fastgwa")

Compute LD matrix:

ldblockurl = "https://bitbucket.org/nygcresearch/ldetect-data/raw/ac125e47bf7ff3e90be31f278a7b6a61daaba0dc/EUR/fourierls-all.bed" gdl.computeld('block', ldblocksfile=ldblockurl, dtype='int16', computespectralproperties=True, outputdir='temp/blockld/')

Initialize Lasso model:

lasso_model = Lasso(gdl, lam=100)

Perform model fit:

lasso_model.fit()

```

Citation

If you use this package in your research, please cite the following paper:

```bibtex

@article {Song2025.01.28.25321292, author = {Song, Junyi and Zabad, Shadi and Yang, Archer and Li, Yue}, title = {Sparse Polygenic Risk Score Inference with the Spike-and-Slab LASSO}, elocation-id = {2025.01.28.25321292}, year = {2025}, doi = {10.1101/2025.01.28.25321292}, publisher = {Cold Spring Harbor Laboratory Press}, URL = {https://www.medrxiv.org/content/early/2025/01/29/2025.01.28.25321292}, eprint = {https://www.medrxiv.org/content/early/2025/01/29/2025.01.28.25321292.full.pdf}, journal = {medRxiv} }

```

Owner

Name: Shadi
Login: shz9
Kind: user

Website: https://shz9.github.io/
Repositories: 20
Profile: https://github.com/shz9

PhD Student at McGill University

Citation (CITATION.md)

If you use `penprs` in your research, please cite the following paper:

```bibtex

@article {Song2025.01.28.25321292,
	author = {Song, Junyi and Zabad, Shadi and Yang, Archer and Li, Yue},
	title = {Sparse Polygenic Risk Score Inference with the Spike-and-Slab LASSO},
	elocation-id = {2025.01.28.25321292},
	year = {2025},
	doi = {10.1101/2025.01.28.25321292},
	publisher = {Cold Spring Harbor Laboratory Press},
	URL = {https://www.medrxiv.org/content/early/2025/01/29/2025.01.28.25321292},
	eprint = {https://www.medrxiv.org/content/early/2025/01/29/2025.01.28.25321292.full.pdf},
	journal = {medRxiv}
}

```

GitHub Events

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Last Year

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Last synced: 6 months ago

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Past Year

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