LEA
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see LEA.
LEA: an R package for Landscape and Ecological Association Studies
Bioconductor version: 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>
citation("LEA")):
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")| LEA: An R Package for Landscape and Ecological Association Studies | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, Regression, Software, Statistical Method |
| Version | 3.6.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 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 |
See More
| 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_3.6.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/LEA/ |
| Package Short Url | https://bioconductor.org/packages/LEA/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |