Files in stephenslab/susiF.alpha
Sum of Single Functions
.Rbuildignore
.gitattributes
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/EBmvFR.R
R/EBmvFR_workhorse.R
R/ELBO.R
R/EM.R
R/Simulations_functions.R
R/SuSiF-package.R
R/ash_utility.R
R/computational_functions.R
R/operation_on_EBmvFR_obj.R
R/operation_on_prior.R
R/operation_on_susiF_obj.R
R/plot_functions.R
R/susiF.R
R/susiF_workhorse.R
R/utils.R
R/wavelet_utils.R
README.md
_pkgdown.yml
docs/404.html
docs/LICENSE-text.html
docs/articles/Adjusting_covariate.html
docs/articles/Adjusting_covariate_files/figure-html/unnamed-chunk-3-1.png
docs/articles/Adjusting_covariate_files/figure-html/unnamed-chunk-4-1.png
docs/articles/Adjusting_covariate_files/figure-html/unnamed-chunk-5-1.png
docs/articles/Adjusting_covariate_files/figure-html/unnamed-chunk-7-1.png
docs/articles/Adjusting_covariate_files/figure-html/unnamed-chunk-7-2.png
docs/articles/Adjusting_covariate_files/figure-html/unnamed-chunk-9-1.png
docs/articles/Adjusting_covariate_files/figure-html/unnamed-chunk-9-2.png
docs/articles/Coloc_fsusie.html
docs/articles/Coloc_fsusie_files/figure-html/setup-1.png
docs/articles/Limitation_SuSiE.html
docs/articles/Limitation_SuSiE_files/figure-html/unnamed-chunk-2-1.png
docs/articles/Limitation_SuSiE_files/figure-html/unnamed-chunk-4-1.png
docs/articles/Limitation_SuSiE_files/figure-html/unnamed-chunk-5-1.png
docs/articles/fsusie_intro.html
docs/articles/fsusie_intro_files/figure-html/plot-all-1.png
docs/articles/fsusie_intro_files/figure-html/plot-effects-1.png
docs/articles/fsusie_intro_files/figure-html/plot-effects-uneven-1.png
docs/articles/fsusie_intro_files/figure-html/plot-pips-1.png
docs/articles/fsusie_intro_files/figure-html/sim-effects-1.png
docs/articles/fsusie_intro_files/figure-html/sim-effects-uneven-1.png
docs/articles/index.html
docs/articles/introduction.html
docs/articles/introduction_files/figure-html/unnamed-chunk-10-1.png
docs/articles/introduction_files/figure-html/unnamed-chunk-11-1.png
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docs/articles/introduction_files/figure-html/unnamed-chunk-7-2.png
docs/articles/introduction_files/figure-html/unnamed-chunk-8-1.png
docs/articles/methyl_demo.html
docs/articles/methyl_demo_files/figure-html/fsusie-affected-cpgs-TI-1.png
docs/articles/methyl_demo_files/figure-html/fsusie-pip-plot-1.png
docs/articles/methyl_demo_files/figure-html/gwas-by-cpg-1.png
docs/articles/methyl_demo_files/figure-html/gwas-by-snp-1.png
docs/articles/methyl_demo_files/figure-html/plot-data-1.png
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/EBmvFR-1.png
docs/reference/EBmvFR-2.png
docs/reference/EBmvFR-3.png
docs/reference/EBmvFR-4.png
docs/reference/EBmvFR.html
docs/reference/EBmvFR.workhorse.html
docs/reference/Eloglik.html
docs/reference/HMM_regression.html
docs/reference/L_mixsq.html
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/Rplot003.png
docs/reference/Rplot004.png
docs/reference/Rplot005.png
docs/reference/TI_regression.html
docs/reference/affected_reg.html
docs/reference/cal_KL_l.html
docs/reference/cal_clfsr.html
docs/reference/cal_cor_cs.html
docs/reference/cal_lfsr.html
docs/reference/cal_lik.html
docs/reference/cal_partial_resid.html
docs/reference/cal_purity.html
docs/reference/cal_zeta.html
docs/reference/check_cs.html
docs/reference/colScale.html
docs/reference/discard_cs.html
docs/reference/estimate_residual_variance.html
docs/reference/gen_wavelet_indx-1.png
docs/reference/gen_wavelet_indx.html
docs/reference/get_ER2.html
docs/reference/get_G_prior.html
docs/reference/get_fitted_effect.html
docs/reference/get_objective.html
docs/reference/get_pi0.html
docs/reference/get_pi_G_prior.html
docs/reference/get_sd_G_prior.html
docs/reference/greedy_backfit.html
docs/reference/index.html
docs/reference/init_EBmvFR_obj.html
docs/reference/init_prior.default.html
docs/reference/init_prior.html
docs/reference/init_susiF_obj.html
docs/reference/log_BF.html
docs/reference/loglik_SFR.html
docs/reference/loglik_SFR_post.html
docs/reference/m_step.html
docs/reference/merge_effect.html
docs/reference/out_prep.html
docs/reference/plot_effect_susiF.html
docs/reference/plot_susiF.html
docs/reference/post_mat_mean.html
docs/reference/post_mat_sd.html
docs/reference/remap_data.html
docs/reference/simu_IBSS_ash_vanilla-1.png
docs/reference/simu_IBSS_ash_vanilla.html
docs/reference/simu_IBSS_per_level-1.png
docs/reference/simu_IBSS_per_level.html
docs/reference/susiF-1.png
docs/reference/susiF-2.png
docs/reference/susiF-3.png
docs/reference/susiF-4.png
docs/reference/susiF-5.png
docs/reference/susiF.html
docs/reference/susiF.workhorse.html
docs/reference/test_stop_cond.html
docs/reference/update_ELBO.html
docs/reference/update_KL.html
docs/reference/update_alpha.html
docs/reference/update_alpha_hist.html
docs/reference/update_ash_pi.html
docs/reference/update_cal_cs.html
docs/reference/update_cal_fit_func.html
docs/reference/update_cal_pip.html
docs/reference/update_lBF.html
docs/reference/update_lfsr.html
docs/reference/update_lfsr_effect.html
docs/reference/update_prior.html
docs/reference/update_residual_variance.html
docs/reference/which_dummy_cs.html
docs/reference/which_lowcount.html
docs/sitemap.xml
inst/code/checl_susie_small.R
inst/code/test_smoot_sparse_reg.R
man/EBmvFR.Rd
man/EBmvFR.workhorse.Rd
man/Eloglik.Rd
man/HMM_regression.Rd
man/L_mixsq.Rd
man/TI_regression.Rd
man/affected_reg.Rd
man/cal_KL_l.Rd
man/cal_clfsr.Rd
man/cal_cor_cs.Rd
man/cal_lfsr.Rd
man/cal_lik.Rd
man/cal_partial_resid.Rd
man/cal_purity.Rd
man/cal_zeta.Rd
man/change_fit.Rd
man/check_cs.Rd
man/colScale.Rd
man/discard_cs.Rd
man/estimate_residual_variance.Rd
man/fsusie_plots.Rd
man/gen_wavelet_indx.Rd
man/get_ER2.Rd
man/get_G_prior.Rd
man/get_fitted_effect.Rd
man/get_objective.Rd
man/get_pi0.Rd
man/get_pi_G_prior.Rd
man/get_sd_G_prior.Rd
man/greedy_backfit.Rd
man/init_EBmvFR_obj.Rd
man/init_prior.Rd
man/init_prior.default.Rd
man/init_susiF_obj.Rd
man/log_BF.Rd
man/loglik_SFR.Rd
man/loglik_SFR_post.Rd
man/m_step.Rd
man/merge_effect.Rd
man/out_prep.Rd
man/post_mat_mean.Rd
man/post_mat_sd.Rd
man/remap_data.Rd
man/simu_IBSS_ash_vanilla.Rd
man/simu_IBSS_per_level.Rd
man/smash_regression.Rd
man/susiF.Rd
man/susiF.workhorse.Rd
man/test_stop_cond.Rd
man/update_ELBO.Rd
man/update_KL.Rd
man/update_alpha.Rd
man/update_alpha_hist.Rd
man/update_ash_pi.Rd
man/update_cal_cs.Rd
man/update_cal_fit_func.Rd
man/update_cal_pip.Rd
man/update_lBF.Rd
man/update_lfsr.Rd
man/update_lfsr_effect.Rd
man/update_prior.Rd
man/update_residual_variance.Rd
man/which_dummy_cs.Rd
man/which_lowcount.Rd
pb.RData
susiF.alpha.Rproj
tests/testthat/hmm_unit_test.R
tests/testthat/test_correct_HMM_post.R
tests/testthat/test_mixture_per_scale_prior.R
tests/testthat/test_mixture_prior.R
tests/testthat/test_plot.R
vignettes/Adjusting_covariate.Rmd
vignettes/Coloc_fsusie.Rmd
vignettes/Limitation_SuSiE.Rmd
vignettes/fsusie_intro.Rmd
vignettes/methyl_demo.Rmd
weird_smash.RData
