LEA

LEA: an R package for Landscape and Ecological Association Studies

Bioconductor version: Release (3.19)

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, and also performs imputation of missing genotypes. The package includes statistical methods for estimating ancestry coefficients from large genotypic matrices and for evaluating the number of ancestral populations (snmf). It performs statistical tests using latent factor mixed models for identifying genetic polymorphisms that exhibit association with environmental gradients or phenotypic traits (lfmm2). In addition, LEA computes values of genetic offset statistics based on new or predicted environments (genetic.gap, genetic.offset). LEA is mainly based on optimized programs that can scale with the dimensions 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>

Citation (from within R, enter citation("LEA")):

Installation

To install this package, start R (version "4.4") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, Regression, Software, Statistical Method
Version	3.16.0
In Bioconductor since	BioC 3.1 (R-3.2) (9.5 years)
License	GPL-3
Depends	R (>= 3.3.0), methods, stats, utils, graphics
Imports
System Requirements
URL	http://membres-timc.imag.fr/Olivier.Francois/lea.html

Suggests	knitr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	LEA_3.16.0.tar.gz
Windows Binary (x86_64)	LEA_3.16.0.zip
macOS Binary (x86_64)	LEA_3.16.0.tgz
macOS Binary (arm64)	LEA_3.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/LEA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/LEA
Bioc Package Browser	https://code.bioconductor.org/browse/LEA/
Package Short Url	https://bioconductor.org/packages/LEA/
Package Downloads Report	Download Stats