Snpnet - Efficient Lasso Solver for Large-scale SNP Data

License: GPL-2

Reference:

• Qian, Junyang, Wenfei Du, Yosuke Tanigawa, Matthew Aguirre, Robert Tibshirani, Manuel A. Rivas, and Trevor Hastie. "A Fast and Flexible Algorithm for Solving the Lasso in Large-scale and Ultrahigh-dimensional Problems." bioRxiv (2020): https://www.biorxiv.org/content/10.1101/630079v3
• Ruilin Li, Christopher Chang, Johanne Marie Justesen, Yosuke Tanigawa, Junyang Qian, Trevor Hastie, Manuel A. Rivas, Robert Tibshirani. "Fast Lasso method for Large-scale and Ultrahigh-dimensional Cox Model with applications to UK Biobank." bioRxiv (2020): https://www.biorxiv.org/content/10.1101/2020.01.20.913194v1.full.pdf

Installation:

Most of the requirements of snpnet are available from CRAN. It also depends on the pgenlibr, glmnet/glmnetPlus and cindex (for survival analysis) packages. One can install them by running the following commands in R. Notice that the installation of pgenlibr requires zstd(>=1.4.4). It can be built from source or simply available from conda, pip or brew.

library(devtools)
install_github("junyangq/glmnetPlus")
install_github("chrchang/plink-ng", subdir="/2.0/cindex")
install_github("chrchang/plink-ng", subdir="/2.0/pgenlibr")

We assume the users already have PLINK 2.0. Otherwise it can be installed from https://www.cog-genomics.org/plink/2.0/.