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 07 Mar. 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

testDriveR  
Teaching Data for Statistics and Data Science
Provides data sets for teaching statistics and data science courses. It includes a sample of data f ...
Download / Learn more Package Citations See dependency  
lmSubsets  
Exact Variable-Subset Selection in Linear Regression
Exact and approximation algorithms for variable-subset selection in ordinary linear regression mode ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
portalr  
Create Useful Summaries of the Portal Data
Download and generate summaries for the rodent, plant, ant, and weather data from the Portal Projec ...
Download / Learn more Package Citations See dependency  
SAMtool  
Stock Assessment Methods Toolkit
Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform ...
Download / Learn more Package Citations See dependency  
ReviewR  
A Light-Weight, Portable Tool for Reviewing Individual Patient Records
A portable Shiny tool to explore patient-level electronic health record data and perform chart revi ...
Download / Learn more Package Citations See dependency  

26,264

R Packages

223,360

Dependencies

70,376

Author Associations

26,265

Publication Badges

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