├── .gitignore ├── DESCRIPTION ├── LICENSE ├── Makefile ├── NAMESPACE ├── R ├── Dat.R ├── LfmmDat.R ├── RcppExports.R ├── cross-validation.R ├── example_data.R ├── helpers.R ├── hypothesis-testing.R ├── io.R ├── lassoLFMM.R ├── lfmm.R ├── matrix-factorizationR.R ├── ridgeLFMM.R ├── sampler.R └── skin_exposure.R ├── README.md ├── _pkgdown.yml ├── data ├── example.data.rda └── skin.exposure.rda ├── docs ├── LICENSE.html ├── articles │ ├── index.html │ ├── lfmm.html │ └── lfmm_files │ │ └── figure-html │ │ ├── unnamed-chunk-10-1.png │ │ ├── unnamed-chunk-13-1.png │ │ ├── unnamed-chunk-17-1.png │ │ ├── unnamed-chunk-18-1.png │ │ ├── unnamed-chunk-22-1.png │ │ ├── unnamed-chunk-23-1.png │ │ ├── unnamed-chunk-4-1.png │ │ ├── unnamed-chunk-5-1.png │ │ └── unnamed-chunk-9-1.png ├── authors.html ├── index.html ├── jquery.sticky-kit.min.js ├── link.svg ├── pkgdown.css ├── pkgdown.js └── reference │ ├── Dat.html │ ├── LfmmDat.html │ ├── SimulatedLfmmDat.html │ ├── compute_P.html │ ├── compute_pvalue_from_tscore.html │ ├── compute_pvalue_from_zscore.html │ ├── effect_size-1.png │ ├── effect_size-2.png │ ├── effect_size-3.png │ ├── effect_size.html │ ├── example.data.html │ ├── forward_test-1.png │ ├── forward_test-2.png │ ├── forward_test.html │ ├── hypothesis_testing_lm.html │ ├── index.html │ ├── left.out.kfold.html │ ├── lfmm.html │ ├── lfmm_CV.html │ ├── lfmm_fit.html │ ├── lfmm_fit_knowing_loadings.html │ ├── lfmm_fit_knowing_loadings.ridgeLFMM.html │ ├── lfmm_impute.html │ ├── lfmm_lasso-1.png │ ├── lfmm_lasso-2.png │ ├── lfmm_lasso.html │ ├── lfmm_residual_error2.html │ ├── lfmm_ridge-1.png │ ├── lfmm_ridge-2.png │ ├── lfmm_ridge.html │ ├── lfmm_ridge_CV-1.png │ ├── lfmm_ridge_CV-2.png │ ├── lfmm_ridge_CV.html │ ├── lfmm_sampler.html │ ├── lfmm_test-1.png │ ├── lfmm_test-2.png │ ├── lfmm_test.html │ ├── predict_lfmm-1.png │ ├── predict_lfmm-2.png │ ├── predict_lfmm.html │ └── skin.exposure.html ├── hooks └── post-receive.sh ├── inst └── doc │ ├── lfmm.R │ ├── lfmm.Rmd │ └── lfmm.html ├── man ├── Dat.Rd ├── LfmmDat.Rd ├── SimulatedLfmmDat.Rd ├── compute_P.Rd ├── compute_pvalue_from_tscore.Rd ├── compute_pvalue_from_zscore.Rd ├── effect_size.Rd ├── example.data.Rd ├── forward_test.Rd ├── glm_test.Rd ├── hypothesis_testing_lm.Rd ├── left.out.kfold.Rd ├── lfmm.Rd ├── lfmm_CV.Rd ├── lfmm_fit.Rd ├── lfmm_fit_knowing_loadings.Rd ├── lfmm_fit_knowing_loadings.ridgeLFMM.Rd ├── lfmm_impute.Rd ├── lfmm_lasso.Rd ├── lfmm_residual_error2.Rd ├── lfmm_ridge.Rd ├── lfmm_ridge_CV.Rd ├── lfmm_sampler.Rd ├── lfmm_test.Rd ├── predict_lfmm.Rd └── skin.exposure.Rd ├── src ├── RcppExports.cpp ├── helpers.cpp └── tess3.cpp ├── tests ├── testthat.R └── testthat │ ├── test-dat.R │ ├── test-helpers.R │ ├── test-hypothesis-testing.R │ ├── test-lassoLFMM.R │ ├── test-lfmm.R │ ├── test-ridgeLFMM.R │ ├── test-sampler.R │ └── test-tess3.R └── vignettes └── lfmm.Rmd /.gitignore: -------------------------------------------------------------------------------- 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