locStra
Fast Implementation of (Local) Population Stratification Methods
Fast implementations to compute the genetic covariance matrix, the Jaccard similarity matrix, the s-matrix (the weighted Jaccard similarity matrix), and the (classic or robust) genomic relationship matrix of a (dense or sparse) input matrix (see Hahn, Lutz, Hecker, Prokopenko, Cho, Silverman, Weiss, and Lange (2020) <doi:10.1002/gepi.22356>). Full support for sparse matrices from the R-package 'Matrix'. Additionally, an implementation of the power method (von Mises iteration) to compute the largest eigenvector of a matrix is included, a function to perform an automated full run of global and local correlations in population stratification data, a function to compute sliding windows, and a function to invert minor alleles and to select those variants/loci exceeding a minimal cutoff value. New functionality in locStra allows one to extract the k leading eigenvectors of the genetic covariance matrix, Jaccard similarity matrix, s-matrix, and genomic relationship matrix via fast PCA without actually computing the similarity matrices. The fast PCA to compute the k leading eigenvectors can now also be run directly from 'bed'+'bim'+'fam' files.
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
1.9 |
rolling linux/jammy R-4.5 | locStra_1.9.tar.gz |
245.8 KiB |
1.9 |
rolling linux/noble R-4.5 | locStra_1.9.tar.gz |
254.3 KiB |
1.9 |
rolling source/ R- | locStra_1.9.tar.gz |
46.7 KiB |
1.9 |
latest linux/jammy R-4.5 | locStra_1.9.tar.gz |
245.8 KiB |
1.9 |
latest linux/noble R-4.5 | locStra_1.9.tar.gz |
254.3 KiB |
1.9 |
latest source/ R- | locStra_1.9.tar.gz |
46.7 KiB |
1.9 |
2026-04-26 source/ R- | locStra_1.9.tar.gz |
46.7 KiB |
1.9 |
2026-04-23 source/ R- | locStra_1.9.tar.gz |
46.7 KiB |
1.9 |
2026-04-09 windows/windows R-4.5 | locStra_1.9.zip |
569.5 KiB |
1.9 |
2025-04-20 source/ R- | locStra_1.9.tar.gz |
46.7 KiB |