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.

Version: 1.9
Imports: Rcpp (≥ 0.12.13), Rdpack, Matrix, RSpectra, bigsnpr
LinkingTo: Rcpp, RcppEigen
Published: 2022-04-12
DOI: 10.32614/CRAN.package.locStra
Author: Georg Hahn [aut,cre], Sharon M. Lutz [ctb], Christoph Lange [ctb]
Maintainer: Georg Hahn <ghahn at hsph.harvard.edu>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
CRAN checks: locStra results


Reference manual: locStra.pdf


Package source: locStra_1.9.tar.gz
Windows binaries: r-devel: locStra_1.9.zip, r-release: locStra_1.9.zip, r-oldrel: locStra_1.9.zip
macOS binaries: r-release (arm64): locStra_1.9.tgz, r-oldrel (arm64): locStra_1.9.tgz, r-release (x86_64): locStra_1.9.tgz, r-oldrel (x86_64): locStra_1.9.tgz
Old sources: locStra archive

Reverse dependencies:

Reverse suggests: scPipe


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