README.md

In Iuliana-Ionita-Laza/BIGKnock: BIobank-scale Gene-based association test via Knockoffs

BIGKnock

This is an R package of performing biobank-scale gene-based association test via knockoffs.

Description

The package contain functions for knockoff generation of gene and enhancers under biobank-scale data and conduct gene-based association test for related samples under fitted null GLMM.

Prerequisites

R (recommended version >= 3.6.0)

Dependencies

BIGKnock depends on R packages SKAT, Matrix, MASS, SPAtest, CompQuadForm and irlba. Make sure to install those packages before installing BIGKnock.

SAIGE/SAIGE-Gene package is used for creating sparse GRM and fitting the null GLMMs.

Installation

library(devtools)

devtools::install_github("Iuliana-Ionita-Laza/BIGKnock")

The current version is 0.1 (February 26, 2022).

Usage

Please see the BIGKnock user manual for detailed usage of BIGKnock package.

We implement SAIGE/SAIGE-Gene package for Step 1: Construct the sparse GRM and Step 2: Fit the null GLMMs. Please see the tutorial for more details.

Contact

If you have any questions about BIGKnock please contact

• [e-mail]

If you want to submit a issue concerning the software please do so using the BIGKnock Github repository.

Reference

• Ma, S., Wang, C., Khan, A., Liu, L., Dalgleish, J., Kiryluk, K., He, Z. and Ionita-Laza, I. (2023). "BIGKnock: Fine-mapping gene-based associations via knockoff analysis of biobank-scale data". Genome Biology.
• He, Z., Guen, Y. L., Liu, L., Lee, J., Ma, S., Yang, A. C., Liu. X., Rutledge, J., Losada, P. M., Song, B., Belloy, M. E., Butler, R. R., Longo, F. M., Tang, H., Mormino, E. C., Wyss-Coray, T., Greicius, M. D. and Ionita-Laza, I. (2021) "Genome-wide analysis of common and rare variants via multiple knockoffs at biobank scale, with an application to Alzheimer disease genetics". American Journal of Human Genetics, 108, 2336-2353.

License

This software is licensed under GPLv3.

Iuliana-Ionita-Laza/BIGKnock documentation built on July 31, 2023, 3:50 p.m.