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 26 Aug. 2026.
Previous versions and publish date:
(2026-07-09 07:53), 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

ncodeR  
Techniques for Automated Classifiers
A set of techniques that can be used to develop, validate, and implement automated classifiers. A po ...
Download / Learn more Package Citations See dependency  
leafgl  
High-Performance 'WebGl' Rendering for Package 'leaflet'
Provides bindings to the 'Leaflet.glify' JavaScript library which extends the 'leaflet' JavaScript l ...
Download / Learn more Package Citations See dependency  
RCytoGPS  
Using Cytogenetics Data in R
Defines classes and methods to process text-based cytogenetics using the CytoGPS web site, then imp ...
Download / Learn more Package Citations See dependency  
clinUtils  
General Utility Functions for Analysis of Clinical Data
Utility functions to facilitate the import, the reporting and analysis of clinical data. Example ...
Download / Learn more Package Citations See dependency  
SelvarMix  
Regularization for Variable Selection in Model-Based Clustering and Discriminant Analysis
Performs a regularization approach to variable selection in themodel-based clustering and classifica ...
Download / Learn more Package Citations See dependency  
PCADSC  
Tools for Principal Component Analysis-Based Data Structure Comparisons
A suite of non-parametric, visual tools for assessing differences in data structures for two datase ...
Download / Learn more Package Citations See dependency  

28,332

R Packages

239,283

Dependencies

75,113

Author Associations

28,333

Publication Badges

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