Files in jean997/cause
CAUSE: Causal Analysis Using Summary Effect Estimates
.Rbuildignore
.Rprofile
.gitignore
DESCRIPTION
NAMESPACE
R/RcppExports.R
R/Z_post.R
R/cause.R
R/cause_download_example_gwas_data.R
R/cause_grid_adapt.R
R/compute_genetic_correlation.R
R/est_cause_params.R
R/est_cause_params_future.R
R/eta_gamma_prior.R
R/gwas_format.R
R/gwas_merge.R
R/in_sample_elpd_loo.R
R/ld_prune.R
R/map_pi_rho.R
R/map_pi_rho_nonnull.R
R/map_pi_rho_nonnull_eqg.R
R/map_pi_rho_nonnull_fixed.R
R/map_pi_rho_nonnull_geq.R
R/map_pi_rho_nonnull_qge.R
R/marge_dists.R
R/package.R
R/plot.R
R/samp_from_grid.R
R/setup_cause_pipeline.R
R/setup_gwas_pairs.R
R/step_quantile.R
R/summary.R
README.md
_workflowr.yml
analysis/_site.yml
analysis/about.Rmd
analysis/cause.bib
analysis/explore.Rmd
analysis/figure/simulations.Rmd/plot_fp-1.png
analysis/figure/simulations.Rmd/roc-1.png
analysis/figure/simulations.Rmd/unnamed-chunk-3-1.png
analysis/figure/simulations.Rmd/unnamed-chunk-5-1.png
analysis/figure/simulations.Rmd/unnamed-chunk-6-1.png
analysis/gwas_pairs.Rmd
analysis/gwas_pairs_2.Rmd
analysis/index.Rmd
analysis/ldl_cad.Rmd
analysis/license.Rmd
analysis/little_test.Rmd
analysis/mrcieu.Rmd
analysis/pipeline.Rmd
analysis/simulations.Rmd
cause.Rproj
code/README.md
code/extract_results_main.R
code/extract_sigma_g.R
code/summarize_sigma_g.R
docs/.nojekyll
docs/WNAR_2019.pdf
docs/about.html
docs/cause.bib
docs/cause_figure_1_standalone.png
docs/cause_figure_3_standalone.pdf
docs/cause_figure_3_standalone.png
docs/explore.html
docs/figure/ldl_cad.Rmd/plot1-1.png
docs/figure/ldl_cad.Rmd/plot1-2.png
docs/figure/ldl_cad.Rmd/plot2-1.png
docs/figure/ldl_cad.Rmd/plot3-1.png
docs/figure/little_test.Rmd/plot1-1.png
docs/figure/little_test.Rmd/plot1-2.png
docs/figure/little_test.Rmd/plot2-1.png
docs/figure/little_test.Rmd/plot3-1.png
docs/figure/simulations.Rmd/plot_fp-1.png
docs/figure/simulations.Rmd/roc-1.png
docs/figure/simulations.Rmd/unnamed-chunk-3-1.png
docs/figure/simulations.Rmd/unnamed-chunk-5-1.png
docs/figure/simulations.Rmd/unnamed-chunk-6-1.png
docs/fp_2019-12-13.png
docs/gwas_pairs.html
docs/gwas_pairs_2.html
docs/index.html
docs/introduction.html
docs/ldl_cad.html
docs/license.html
docs/little_test.html
docs/mrcieu.html
docs/pipeline.html
docs/pwr_2019-12-13.png
docs/scatter4_updlegend.png
docs/scatter5_updlegend.png
docs/simulations.html
docs/site_libs/bootstrap-3.3.5/css/bootstrap-theme.css
docs/site_libs/bootstrap-3.3.5/css/bootstrap-theme.css.map
docs/site_libs/bootstrap-3.3.5/css/bootstrap-theme.min.css
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example_data/LDL_CAD_merged.RDS
example_data/LDL_CAD_params.RDS
example_data/top_ldl_pruned_plink.RDS
example_data/top_ldl_pruned_vars.RDS
man/Z_post.Rd
man/adapt2_grid.Rd
man/cause.Rd
man/cause_download_example_gwas_data.Rd
man/cause_grid_adapt.Rd
man/est_cause_params.Rd
man/est_cause_params_future.Rd
man/eta_gamma_prior.Rd
man/gwas_format.Rd
man/gwas_merge.Rd
man/in_sample_elpd_loo.Rd
man/ld_prune.Rd
man/loglik.Rd
man/loglik_ij.Rd
man/loglik_loo.Rd
man/loglik_mat.Rd
man/loglik_samps_Z0.Rd
man/loglik_samps_Z1.Rd
man/map_pi_rho.Rd
man/map_pi_rho_nonnull.Rd
man/map_pi_rho_nonnull_eqg.Rd
man/map_pi_rho_nonnull_fixed.Rd
man/map_pi_rho_nonnull_geq.Rd
man/map_pi_rho_nonnull_qge.Rd
man/new_cause_data.Rd
man/new_cause_data_fit.Rd
man/plot.cause.Rd
man/plot.cause_post.Rd
man/print.cause_summary.Rd
man/print.summary_cause_post.Rd
man/recompute_elpd_table.Rd
man/samp_from_grid.Rd
man/setup_cause_pipeline.Rd
man/setup_gwas_pairs.Rd
man/step_quantile.Rd
man/summary.cause.Rd
man/summary.cause_post.Rd
output/README.md
pipeline_code/R/cause.R
pipeline_code/R/cause_params.R
pipeline_code/R/extract_results.R
pipeline_code/R/format_data.R
pipeline_code/R/lcv.R
pipeline_code/R/ld_cat.R
pipeline_code/R/ld_prune_one_chrom.R
pipeline_code/R/ld_prune_plink.R
pipeline_code/R/merge_data.R
pipeline_code/R/mr_package.R
pipeline_code/R/mrpresso.R
pipeline_code/Snakefile
pipeline_code/cluster.yaml
pipeline_code/config.yaml
pipeline_code/gwas_pairs.csv
pipeline_code/run-snakemake.sh
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/log_likelihood_functions.cpp
