Other packages > Find by keyword >

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]
All associated links for this package
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 25 Jun. 2026.
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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

airGRiwrm  
'airGR' Integrated Water Resource Management
Semi-distributed Precipitation-Runoff Modelling based on 'airGR' package models integrating human i ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
foster  
Forest Structure Extrapolation with R
Set of tools to streamline the modeling of the relationship betweensatellite imagery time series or ...
Download / Learn more Package Citations See dependency  
sitmo  
Parallel Pseudo Random Number Generator (PPRNG) 'sitmo' Header Files
Provided within are two high quality and fast PPRNGs that may be used in an 'OpenMP' parallel enviro ...
Download / Learn more Package Citations See dependency  
edeaR  
Exploratory and Descriptive Event-Based Data Analysis
Exploratory and descriptive analysis of event based data. Provides methods for describing and select ...
Download / Learn more Package Citations See dependency  

27,535

R Packages

236,180

Dependencies

73,223

Author Associations

27,536

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA