LEA is an R package dedicated to genomewide association tests in general, with emphasis on association with ecological gradients. LEA also runs analyses of population structure and scans for genomic signatures of local adaptation.
More specifically, LEA includes statistical methods for
- estimating ancestry coefficients from large genotypic matrices, evaluating the number of ancestral populations, performing population differentiation tests of neutrality, and displaying results.
- identifying genetic polymorphisms that exhibit high correlation with environmental gradients or with phenotypic traits, after controlling for confounding effects.
- computing genomic offset statistics that predict fitness values in altered environments.
LEA is mainly based on optimized C programs that can scale with the dimension of large data sets.
This work was supported by a grant (CIBLE2010-14) from
la région Rhône-Alpes.