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lfmm (version 1.1)

Latent Factor Mixed Models

Description

Fast and accurate inference of gene-environment associations (GEA) in genome-wide studies (Caye et al., 2019, ). We developed a least-squares estimation approach for confounder and effect sizes estimation that provides a unique framework for several categories of genomic data, not restricted to genotypes. The speed of the new algorithm is several times faster than the existing GEA approaches, then our previous version of the 'LFMM' program present in the 'LEA' package (Frichot and Francois, 2015, ).

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Version

Install

install.packages('lfmm')

Monthly Downloads

330

Version

1.1

License

GPL-3

Maintainer

Basile Jumentier

Last Published

June 30th, 2021

Functions in lfmm (1.1)

example.data

Genetic and phenotypic data for Arabidopsis thaliana
lfmm

R package : Fast and Accurate statistical methods for adjusting confounding factors in association studies.
lfmm_ridge

LFMM least-squares estimates with ridge penalty
lfmm_test

Statistical tests with latent factor mixed models (linear models)
glm_test

GLM tests with latent factor mixed models
lfmm_sampler

LFMM generative data sampler
effect_size

Direct effect sizes estimated from latent factor models
lfmm_lasso

LFMM least-squares estimates with lasso penalty (Sparse LFMM)
predict_lfmm

Predict polygenic scores from latent factor models
skin.exposure

Simulated (and real) methylation levels for sun exposed patient patients