Files in stephenslab/susieR
Fit Sum of Single Effects Linear Regression Model

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/compute_ss.R R/elbo.R R/elbo_rss.R R/elbo_ss.R R/estimate_residual_variance.R R/initialize.R R/initialize_rss.R R/predict.susie.R R/remove_null_effects.R R/set_R_attributes.R R/set_X_attributes.R R/single_effect_regression.R R/single_effect_regression_rss.R R/single_effect_regression_ss.R R/sparse_multiplication.R R/summary.susie.R R/susie.R R/susie_auto.R R/susie_plot_changepoint.R R/susie_rss.R R/susie_ss.R R/susie_trendfilter.R R/susie_utils.R R/trend_filtering_multiplication.R R/update_each_effect.R R/update_each_effect_rss.R R/update_each_effect_ss.R README.md
_pkgdown.yml
appveyor.yml
data/N2finemapping.RData
data/N3finemapping.CAVIAR.RData
data/N3finemapping.DAP.RData
data/N3finemapping.FINEMAP.RData
data/N3finemapping.RData
docs/LICENSE-text.html
docs/articles/finemapping.html
docs/articles/finemapping_files/figure-html/unnamed-chunk-12-1.png
docs/articles/finemapping_files/figure-html/unnamed-chunk-14-1.png
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docs/articles/finemapping_summary_statistics.html
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docs/articles/finemapping_summary_statistics_files/figure-html/unnamed-chunk-6-1.png
docs/articles/index.html
docs/articles/l0_initialization.html
docs/articles/mwe.html
docs/articles/mwe_files/figure-html/unnamed-chunk-1-1.png
docs/articles/mwe_files/figure-html/unnamed-chunk-2-1.png
docs/articles/sparse_matrix_strategy.html
docs/articles/sparse_matrix_strategy_files/figure-html/unnamed-chunk-10-1.png
docs/articles/sparse_matrix_strategy_files/figure-html/unnamed-chunk-7-1.png
docs/articles/sparse_susie_eval.html
docs/articles/trend_filtering.html
docs/articles/trend_filtering_files/figure-html/unnamed-chunk-2-1.png
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docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/SER_posterior_e_loglik_rss.html
docs/reference/check_projection.html
docs/reference/check_r_matrix.html
docs/reference/check_semi_pd.html
docs/reference/coef.susie.html
docs/reference/compute_MXt.html
docs/reference/compute_Xb.html
docs/reference/compute_Xty.html
docs/reference/compute_ss.html
docs/reference/compute_tf_Xb.html
docs/reference/compute_tf_Xty.html
docs/reference/compute_tf_cm.html
docs/reference/compute_tf_csd.html
docs/reference/compute_tf_d.html
docs/reference/compute_tf_std_d.html
docs/reference/est_V_uniroot.html
docs/reference/estimate_residual_variance.html
docs/reference/estimate_residual_variance_ss.html
docs/reference/estimate_residual_variance_z.html
docs/reference/get_objective.html
docs/reference/get_objective_rss.html
docs/reference/get_objective_ss.html
docs/reference/get_objective_z.html
docs/reference/index.html
docs/reference/is_symmetric_matrix.html
docs/reference/loglik.html
docs/reference/muffled_corr.html
docs/reference/muffled_cov2cor.html
docs/reference/predict.susie.html
docs/reference/set_R_attributes.html
docs/reference/set_X_attributes.html
docs/reference/single_effect_regression.html
docs/reference/single_effect_regression_rss.html
docs/reference/single_effect_regression_ss.html
docs/reference/summary.susie.html
docs/reference/susie.html
docs/reference/susie_auto.html
docs/reference/susie_bhat.html
docs/reference/susie_get_cs.html
docs/reference/susie_get_lfsr.html
docs/reference/susie_get_objective.html
docs/reference/susie_get_pip.html
docs/reference/susie_get_posterior_mean.html
docs/reference/susie_get_posterior_sd.html
docs/reference/susie_get_prior_variance.html
docs/reference/susie_get_residual_variance.html
docs/reference/susie_init_coef.html
docs/reference/susie_plot.html
docs/reference/susie_plot_iteration.html
docs/reference/susie_rss.html
docs/reference/susie_slim.html
docs/reference/susie_ss.html
docs/reference/susie_trendfilter.html
docs/reference/susie_z.html
docs/reference/update_each_effect.html
docs/reference/update_each_effect_rss.html
docs/reference/update_each_effect_ss.html
inst/analysis/optimize.Rmd inst/analysis/test_susie_auto.Rmd inst/analysis/testing.Rmd inst/code/caviar.R
inst/code/dap-g.py
inst/code/finemap.R inst/code/gen_original_results.R
inst/misc/post-commit.sh
inst/misc/pre-commit.sh
man/SER_posterior_e_loglik_rss.Rd man/check_projection.Rd man/check_semi_pd.Rd man/coef.susie.Rd man/compute_MXt.Rd man/compute_Xb.Rd man/compute_Xty.Rd man/compute_colSds.Rd man/compute_ss.Rd man/compute_tf_Xb.Rd man/compute_tf_Xty.Rd man/compute_tf_cm.Rd man/compute_tf_csd.Rd man/compute_tf_d.Rd man/compute_tf_std_d.Rd man/est_V_uniroot.Rd man/estimate_mad_residual_variance.Rd man/estimate_residual_variance.Rd man/estimate_residual_variance_ss.Rd man/get_objective.Rd man/get_objective_rss.Rd man/get_objective_ss.Rd man/is_symmetric_matrix.Rd man/loglik.Rd man/muffled_corr.Rd man/muffled_cov2cor.Rd man/predict.susie.Rd man/set_R_attributes.Rd man/set_X_attributes.Rd man/single_effect_regression.Rd man/single_effect_regression_rss.Rd man/single_effect_regression_ss.Rd man/summary.susie.Rd man/susie.Rd man/susie_auto.Rd man/susie_bhat.Rd man/susie_get_cs.Rd man/susie_get_lfsr.Rd man/susie_get_objective.Rd man/susie_get_pip.Rd man/susie_get_posterior_mean.Rd man/susie_get_posterior_sd.Rd man/susie_get_prior_variance.Rd man/susie_get_residual_variance.Rd man/susie_init_coef.Rd man/susie_plot.Rd man/susie_plot_changepoint.Rd man/susie_plot_iteration.Rd man/susie_rss.Rd man/susie_slim.Rd man/susie_ss.Rd man/susie_trendfilter.Rd man/update_each_effect.Rd man/update_each_effect_rss.Rd man/update_each_effect_ss.Rd
susieR.Rproj
tests/README.md tests/testthat.R
tests/testthat/ER2_original_res.rds
tests/testthat/Eloglik_original_res.rds
tests/testthat/SER_original_res.rds
tests/testthat/est_V_debug.rds
tests/testthat/helper_testthat.R
tests/testthat/objective_original_res.rds
tests/testthat/singleReg_original_res.rds
tests/testthat/susiefit_original_res.rds
tests/testthat/susiefit_original_res2.rds
tests/testthat/susiefit_original_res3.rds
tests/testthat/susiefit_original_res4.rds
tests/testthat/test_Eloglik.R tests/testthat/test_SER_posterior_e_loglik.R tests/testthat/test_comput_tf.R tests/testthat/test_est_V.R tests/testthat/test_get_ER2.R tests/testthat/test_get_pip.R tests/testthat/test_intercept_standardize.R tests/testthat/test_null_weight.R tests/testthat/test_prior_weights.R tests/testthat/test_single_effect_regression.R tests/testthat/test_sparse_multiplication.R tests/testthat/test_sparse_safe_colScale.R tests/testthat/test_susie.R tests/testthat/test_susie_get_objective.R tests/testthat/test_susie_ss.R tests/testthat/test_susie_ss_bhat.R tests/testthat/test_susie_trendfilter.R tests/testthat/test_update_each_effect.R
tests/testthat/vbupdate_original_res.rds
vignettes/finemapping_demo.Rmd vignettes/finemapping_summary_statistics.Rmd vignettes/l0_initialization.Rmd vignettes/mwe.Rmd vignettes/sparse_matrix_strategy.Rmd vignettes/sparse_susie_eval.Rmd vignettes/trend_filtering.Rmd
vignettes/trendfiltering_derivations.Rnw
vignettes/trendfiltering_derivations.bib
stephenslab/susieR documentation built on Nov. 6, 2019, 1:09 p.m.