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locStra  

Fast Implementation of (Local) Population Stratification Methods
View on CRAN: Click here


Download and install locStra package within the R console
Install from CRAN:
install.packages("locStra")

Install from Github:
library("remotes")
install_github("cran/locStra")

Install by package version:
library("remotes")
install_version("locStra", "1.9")



Attach the package and use:
library("locStra")
Maintained by
Georg Hahn
[Scholar Profile | Author Map]
First Published: 2019-10-11
Latest Update: 2022-04-12
Description:
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) ). 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.
How to cite:
Georg Hahn (2019). locStra: Fast Implementation of (Local) Population Stratification Methods. R package version 1.9, https://cran.r-project.org/web/packages/locStra. Accessed 01 Apr. 2025.
Previous versions and publish date:
1.0 (2019-10-11 11:20), 1.1 (2019-11-26 19:00), 1.2 (2020-01-08 05:40), 1.3 (2020-02-26 07:40), 1.4 (2020-06-14 18:30), 1.5 (2020-12-02 08:40), 1.6 (2020-12-15 23:50), 1.7 (2021-01-27 10:10), 1.8 (2022-02-17 19:12)
Other packages that cited locStra R package
View locStra citation profile
Other R packages that locStra depends, imports, suggests or enhances
Complete documentation for locStra
Functions, R codes and Examples using the locStra R package
Some associated functions: bed_fastCovEVs . bed_fastGrmEVs . bed_fastJaccardEVs . bed_fastSMatrixEVs . covMatrix . fastCovEVs . fastGrmEVs . fastJaccardEVs . fastSMatrixEVs . fullscan . grMatrix . jaccardMatrix . makeWindows . powerMethod . sMatrix . selectVariants . testdata-data . 
Some associated R codes: RcppExports.R . testdata.R .  Full locStra package functions and examples
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