Files in RajLabMSSM/echofinemap

echoverse module: Fine-mapping functions

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md NEWS.md R/ABF.R R/COJO.R R/COJO_args.R R/COJO_check_version.R R/COJO_find_executable.R R/COJO_get_conditional_results.R R/COJO_get_stepwise_results.R R/COJO_list_files.R R/COJO_locus_subdir.R R/COJO_process_results.R R/COJO_run.R R/FINEMAP.R R/FINEMAP_check_existing_results.R R/FINEMAP_check_files.R R/FINEMAP_check_version.R R/FINEMAP_check_version_results.R R/FINEMAP_construct_data.R R/FINEMAP_construct_datak.R R/FINEMAP_construct_master.R R/FINEMAP_find_executable.R R/FINEMAP_import_data_config.R R/FINEMAP_import_data_cred.R R/FINEMAP_import_data_snp.R R/FINEMAP_import_log.R R/FINEMAP_process_results.R R/FINEMAP_run.R R/PAINTOR.R R/PAINTOR_check_ld.R R/PAINTOR_check_populations.R R/PAINTOR_check_required_cols.R R/PAINTOR_check_version.R R/PAINTOR_create_locus_file.R R/PAINTOR_dat_to_list.R R/PAINTOR_datatype_handler.R R/PAINTOR_download_annotations.R R/PAINTOR_find_executable.R R/PAINTOR_find_folder.R R/PAINTOR_get_suffixes.R R/PAINTOR_help.R R/PAINTOR_input_file.R R/PAINTOR_install.R R/PAINTOR_is_installed.R R/PAINTOR_merge_datasets.R R/PAINTOR_prepare_annotations.R R/PAINTOR_prepare_ld_multiancestry.R R/PAINTOR_process_results.R R/PAINTOR_run.R R/PAINTOR_sample_data.R R/POLYFUN.R R/POLYFUN_check_method.R R/POLYFUN_check_mode.R R/POLYFUN_check_version.R R/POLYFUN_compute_priors.R R/POLYFUN_download_ref_files.R R/POLYFUN_example_sumstats.R R/POLYFUN_find_polyfun_folder.R R/POLYFUN_finemapper.R R/POLYFUN_gather_annot_proportions.R R/POLYFUN_gather_annotations.R R/POLYFUN_gather_ldscores.R R/POLYFUN_get_ref_prefix.R R/POLYFUN_help.R R/POLYFUN_import_priors.R R/POLYFUN_import_priors_handler.R R/POLYFUN_initialize.R R/POLYFUN_install.R R/POLYFUN_munge_summ_stats.R R/POLYFUN_prepare_snp_input.R R/POLYFUN_read_priors.R R/POLYFUN_run_ldsc.R R/POLYFUN_sample_size_arg.R R/SUSIE.R R/SUSIE_args_interpreter.R R/SUSIE_check_args.R R/SUSIE_extract_cs.R R/SUSIE_get_func.R R/SUSIE_plot_track.R R/SUSIE_run.R R/Zscore.R R/Zscore_sumstats.R R/check_args.R R/check_required_cols.R R/collapse_args.R R/create_method_path.R R/drop_finemap_cols.R R/exists_not_empty.R R/finemap_args_interpreter.R R/get_data.R R/get_pheno_variance.R R/install_submodule_git.R R/is_32bit.R R/lfm.R R/messager.R R/multifinemap.R R/multifinemap_handler.R R/multifinemap_handler_method.R R/normalize_priors.R R/prepare_priors.R R/preview_data.R R/rbind_filelist.R R/remove_dup_snps.R R/remove_na_rows.R R/required_cols.R R/save_finemap_results.R R/setup_gcc.R R/zzz.R README.Rmd README.md inst/hex/hexSticker.Rmd man/ABF.Rd man/COJO.Rd man/COJO_args.Rd man/COJO_find_executable.Rd man/COJO_get_stepwise_results.Rd man/COJO_locus_subdir.Rd man/COJO_process_results.Rd man/COJO_run.Rd man/FINEMAP.Rd man/FINEMAP_construct_data.Rd man/FINEMAP_construct_master.Rd man/FINEMAP_find_executable.Rd man/FINEMAP_import_log.Rd man/FINEMAP_process_results.Rd man/PAINTOR.Rd man/PAINTOR_create_locus_file.Rd man/PAINTOR_datatype_handler.Rd man/PAINTOR_download_annotations.Rd man/PAINTOR_install.Rd man/PAINTOR_prepare_annotations.Rd man/PAINTOR_prepare_ld_multiancestry.Rd man/PAINTOR_process_results.Rd man/PAINTOR_run.Rd man/PAINTOR_sample_data.Rd man/POLYFUN.Rd man/POLYFUN_check_version.Rd man/POLYFUN_compute_priors.Rd man/POLYFUN_download_ref_files.Rd man/POLYFUN_find_folder.Rd man/POLYFUN_finemapper.Rd man/POLYFUN_gather_annotations.Rd man/POLYFUN_gather_ldscores.Rd man/POLYFUN_help.Rd man/POLYFUN_import_priors.Rd man/POLYFUN_initialize.Rd man/POLYFUN_install.Rd man/POLYFUN_munge_summ_stats.Rd man/POLYFUN_prepare_snp_input.Rd man/POLYFUN_read_priors.Rd man/POLYFUN_run_ldsc.Rd man/SUSIE.Rd man/SUSIE_get_func.Rd man/SUSIE_run.Rd man/check_args.Rd man/check_required_cols.Rd man/create_method_path.Rd man/drop_finemap_cols.Rd man/get_data.Rd man/get_pheno_variance.Rd man/install_submodule_git.Rd man/is_32bit.Rd man/lfm.Rd man/multifinemap.Rd man/multifinemap_handler.Rd man/multifinemap_handler_method.Rd man/prepare_priors.Rd man/rbind_filelist.Rd man/remove_dup_snps.Rd man/remove_na_rows.Rd man/required_cols.Rd man/setup_gcc.Rd tests/testthat.R tests/testthat/test-ABF.R tests/testthat/test-COJO.R tests/testthat/test-FINEMAP.R tests/testthat/test-PAINTOR.R tests/testthat/test-POLYFUN.R tests/testthat/test-POLYFUN_compute_priors.R tests/testthat/test-POLYFUN_help.R tests/testthat/test-SUSIE.R tests/testthat/test-check_required_cols.R tests/testthat/test-multifinemap.R vignettes/echofinemap.Rmd