DOI: 10.18129/B9.bioc.LEA  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see LEA.

LEA: an R package for Landscape and Ecological Association Studies

Bioconductor version: 3.17

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>

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biocViews Clustering, Regression, Software, Statistical Method
Version 3.12.2
In Bioconductor since BioC 3.1 (R-3.2) (8.5 years)
License GPL-3
Depends R (>= 3.3.0), methods, stats, utils, graphics
Suggests knitr
URL http://membres-timc.imag.fr/Olivier.Francois/lea.html
Depends On Me
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