The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

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

Documentation:

Reference manual: locStra.pdf

Downloads:

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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=locStra to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.