LEA

DOI: 10.18129/B9.bioc.LEA    

LEA: an R package for Landscape and Ecological Association Studies

Bioconductor version: Release (3.14)

LEA is an R package dedicated to population genomics, landscape genomics and genotype-environment association tests. LEA can run analyses of population structure and genome-wide tests for local adaptation. The package includes statistical methods for estimating ancestry coefficients from large genotypic matrices and for evaluating the number of ancestral populations (snmf, pca). It performs statistical tests using latent factor mixed models for identifying genetic polymorphisms that exhibit association with environmental gradients or phenotypic traits (lfmm2). {\tt LEA} also performs imputation of missing genotypes, and computes predictive values of genetic offsets based on new or future environments. The package includes factor methods for estimating ancestry coefficients from large genotypic matrices and for evaluating the number of ancestral populations (snmf, pca). LEA is mainly based on optimized programs that can scale with the dimension of large data sets.

Author: Eric Frichot <eric.frichot at gmail.com>, Olivier Francois <olivier.francois at grenoble-inp.fr>, Clement Gain <clement.gain at univ-grenoble-alpes.fr>

Maintainer: Olivier Francois <olivier.francois at grenoble-inp.fr>, Eric Frichot <eric.frichot at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("LEA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("LEA")

 

PDF	R Script	LEA: An R Package for Landscape and Ecological Association Studies
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, Regression, Software, Statistical Method
Version	3.6.0
In Bioconductor since	BioC 3.1 (R-3.2) (7 years)
License	GPL-3
Depends	R (>= 3.3.0), methods, stats, utils, graphics
Imports
LinkingTo
Suggests	knitr
SystemRequirements
Enhances
URL	http://membres-timc.imag.fr/Olivier.Francois/lea.html
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	LEA_3.6.0.tar.gz
Windows Binary	LEA_3.6.0.zip
macOS 10.13 (High Sierra)	LEA_3.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/LEA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/LEA
Package Short Url	https://bioconductor.org/packages/LEA/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive