Files in richelbilderbeek/plinkr
Interface to PLINK
.Rbuildignore
.appveyor.yml
.github/.github/ISSUE_TEMPLATE/bug_report.md
.github/.github/ISSUE_TEMPLATE/custom.md
.github/.github/ISSUE_TEMPLATE/feature_request.md
.github/.github/workflows/R-CMD-check.yaml
.github/.github/workflows/build_singularity.yaml
.github/.github/workflows/check_bash_style.yaml
.github/.github/workflows/check_links.yaml
.github/.github/workflows/check_versions_match.yaml
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/custom.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/R-CMD-check.yaml
.github/workflows/build_singularity.yaml
.github/workflows/check_bash_style.yaml
.github/workflows/check_links.yaml
.github/workflows/check_versions_match.yaml
.gitignore
CODE_OF_CONDUCT.md
CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/assoc.R
R/assoc_adjust_from_bfile.R
R/assoc_from_bfile.R
R/assoc_qt.R
R/assoc_qt_covar.R
R/assoc_qt_on_plink2_bin_data.R
R/assoc_qt_on_plink2_bin_files.R
R/assoc_qt_on_plink_bin_data.R
R/assoc_qt_on_plink_bin_files.R
R/assoc_qt_on_plink_text_data.R
R/assoc_qt_on_plink_text_files.R
R/calc_additive_phenotype_values.R
R/calc_dominant_phenotype_values.R
R/calc_epistatic_phenotype_values.R
R/calc_random_case_control_phenotype_values.R
R/calc_random_phenotype_values.R
R/calc_rnorm_phenotype_values.R
R/calc_runif_phenotype_values.R
R/can_plink_version_and_data_can_work_together.R
R/check_allow_no_sex.R
R/check_assoc_data.R
R/check_assoc_params.R
R/check_assoc_qt_covar_data.R
R/check_assoc_qt_covar_params.R
R/check_assoc_qt_data.R
R/check_assoc_qt_params.R
R/check_assoc_qt_result.R
R/check_assoc_table.R
R/check_base_input_filename.R
R/check_base_output_filename.R
R/check_bed_table.R
R/check_bim_table.R
R/check_calc_phenotype_function.R
R/check_chromosome_number.R
R/check_chromosome_selector.R
R/check_confidence_interval.R
R/check_cov_table.R
R/check_data.R
R/check_empty_plinkr_folder.R
R/check_equal_number_of_snvs.R
R/check_fam_filename.R
R/check_fam_table.R
R/check_fid.R
R/check_fids.R
R/check_iid.R
R/check_iids.R
R/check_ld_window_r2.R
R/check_maf.R
R/check_mafs.R
R/check_map_table.R
R/check_n_individuals.R
R/check_n_samples.R
R/check_n_snps.R
R/check_os.R
R/check_pca_result_filenames.R
R/check_ped_table.R
R/check_pgen_table.R
R/check_phe_file_ok_for_qt.R
R/check_phe_filename.R
R/check_phe_table.R
R/check_phe_table_ok_for_qt.R
R/check_phenotype_data.R
R/check_phenotype_data_filename.R
R/check_phenotype_data_table.R
R/check_phenotypes.R
R/check_plink2_bin_data.R
R/check_plink2_bin_filenames.R
R/check_plink_args.R
R/check_plink_bin_data.R
R/check_plink_bin_filenames.R
R/check_plink_filenames.R
R/check_plink_is_installed.R
R/check_plink_options.R
R/check_plink_optionses.R
R/check_plink_text_data.R
R/check_plink_text_filenames.R
R/check_plink_version.R
R/check_plink_version_and_data_can_work_together.R
R/check_psam_table.R
R/check_pvar_table.R
R/check_qassoc_table.R
R/check_random_samples_selector.R
R/check_random_snps_selector.R
R/check_sample_ids.R
R/check_sample_ids_filename.R
R/check_sample_selector.R
R/check_simulate_qt_params.R
R/check_single_sample_selector.R
R/check_single_snp_selector.R
R/check_snp.R
R/check_snp_range_selector.R
R/check_snp_selector.R
R/check_snp_window_selector.R
R/check_snvs.R
R/check_trait.R
R/check_traits.R
R/check_verbose.R
R/check_window_kb.R
R/clear_plink_folder.R
R/clear_plinkr_cache.R
R/compare_assoc_qt_speed.R
R/convert_bed_table_to_pgen_table.R
R/convert_bim_table_to_map_table.R
R/convert_pgen_table_to_bed_table.R
R/convert_plink2_bin_data_to_plink_bin_data.R
R/convert_plink2_bin_data_to_plink_text_data.R
R/convert_plink2_bin_files_to_plink_bin_files.R
R/convert_plink2_bin_files_to_plink_text_files.R
R/convert_plink_bin_data_to_ped_table.R
R/convert_plink_bin_data_to_plink2_bin_data.R
R/convert_plink_bin_data_to_plink_text_data.R
R/convert_plink_bin_files_to_plink2_bin_files.R
R/convert_plink_bin_files_to_plink_text_files.R
R/convert_plink_bin_files_to_plink_vcf_files.R
R/convert_plink_text_data_to_plink2_bin_data.R
R/convert_plink_text_data_to_plink_bin_data.R
R/convert_plink_text_files_to_plink2_bin_files.R
R/convert_plink_text_files_to_plink_bin_files.R
R/convert_psam_table_to_fam_table.R
R/convert_pvar_table_to_bim_table.R
R/create_additive_trait.R
R/create_assoc_args.R
R/create_assoc_data.R
R/create_assoc_params.R
R/create_assoc_qt_args.R
R/create_assoc_qt_args_on_plink2_bin_data.R
R/create_assoc_qt_args_on_plink2_bin_filenames.R
R/create_assoc_qt_args_on_plink_bin_data.R
R/create_assoc_qt_args_on_plink_bin_filenames.R
R/create_assoc_qt_args_on_plink_text_data.R
R/create_assoc_qt_args_on_plink_text_filenames.R
R/create_assoc_qt_covar_args.R
R/create_assoc_qt_covar_data.R
R/create_assoc_qt_covar_params.R
R/create_assoc_qt_data.R
R/create_assoc_qt_params.R
R/create_bgen_files_for_saige.R
R/create_chromosome_selector.R
R/create_convert_plink_bin_files_to_plink_text_files_args.R
R/create_cov_table_from_data.R
R/create_cov_table_from_ped_table.R
R/create_custom_plink_options.R
R/create_custom_trait.R
R/create_demo_assoc_data.R
R/create_demo_assoc_qt_covar_data.R
R/create_demo_assoc_qt_data.R
R/create_demo_map_table.R
R/create_demo_ped_table.R
R/create_demo_ped_table_lhs.R
R/create_demo_ped_table_rhs.R
R/create_demo_ped_table_rhs_trait.R
R/create_demo_phenotype_table.R
R/create_demo_phenotype_table_lhs.R
R/create_demo_phenotype_table_rhs.R
R/create_demo_traits.R
R/create_dominant_trait.R
R/create_epistatic_trait.R
R/create_keep_args.R
R/create_pca_args.R
R/create_phe_table_from_data.R
R/create_phe_table_from_fam_table.R
R/create_phe_table_from_ped_table.R
R/create_phe_table_from_plink2_bin_data.R
R/create_phe_table_from_plink_bin2_filenames.R
R/create_phe_table_from_plink_bin_data.R
R/create_phe_table_from_plink_bin_filenames.R
R/create_phe_table_from_plink_text_data.R
R/create_phe_table_from_plink_text_filenames.R
R/create_phe_table_from_psam_table.R
R/create_phenotype_data_filename.R
R/create_phenotype_data_table.R
R/create_phenotype_data_table_from_data.R
R/create_plink2_bin_data.R
R/create_plink2_bin_filenames.R
R/create_plink_bin_data.R
R/create_plink_bin_filenames.R
R/create_plink_options.R
R/create_plink_optionses.R
R/create_plink_text_data.R
R/create_plink_text_filenames.R
R/create_plink_v1_7_options.R
R/create_plink_v1_9_options.R
R/create_plink_v2_0_options.R
R/create_random_case_control_trait.R
R/create_random_samples_selector.R
R/create_random_snps_selector.R
R/create_random_trait.R
R/create_rnorm_trait.R
R/create_runif_trait.R
R/create_samples_selector.R
R/create_select_chromosome_args.R
R/create_select_random_samples_args.R
R/create_select_random_snp_args.R
R/create_select_samples_args.R
R/create_select_single_sample_args.R
R/create_select_single_snp_args.R
R/create_select_snp_range_args.R
R/create_select_snp_window_args.R
R/create_select_snps_args.R
R/create_selected_sample_ids.R
R/create_simulate_qt_params.R
R/create_single_sample_selector.R
R/create_single_snp_selector.R
R/create_snp_range_selector.R
R/create_snp_window_selector.R
R/create_snps_selector.R
R/create_snvs.R
R/create_test_assoc_data.R
R/create_test_assoc_params.R
R/create_test_assoc_qt_covar_data.R
R/create_test_assoc_qt_covar_params.R
R/create_test_assoc_qt_data.R
R/create_test_assoc_qt_params.R
R/create_test_chromosome_selector.R
R/create_test_pca_result_filenames.R
R/create_test_phenotype_data_filename.R
R/create_test_phenotype_data_table.R
R/create_test_plink2_bin_data.R
R/create_test_plink2_bin_filenames.R
R/create_test_plink_bin_data.R
R/create_test_plink_bin_filenames.R
R/create_test_plink_text_data.R
R/create_test_plink_text_filenames.R
R/create_test_random_samples_selector.R
R/create_test_random_snp_selector.R
R/create_test_simulate_qt_params.R
R/create_test_single_sample_selector.R
R/create_test_single_snp_selector.R
R/create_test_snp_range_selector.R
R/create_test_snp_selector.R
R/create_trait.R
R/default_params_doc.R
R/do_plink_self_test.R
R/filter_random_snps.R
R/freq_from_bfile_within_phe_file.R
R/freq_from_bfiles.R
R/get_data_description.R
R/get_default_plink_exe_path.R
R/get_default_plink_version.R
R/get_heightest_maf.R
R/get_lowest_maf.R
R/get_marker_correlation_coefficients.R
R/get_marker_correlation_coefficients_table.R
R/get_minor_alelle_frequencies.R
R/get_n_samples.R
R/get_n_snps.R
R/get_os.R
R/get_phenotypes.R
R/get_plink1_versions.R
R/get_plink2_versions.R
R/get_plink_download_url.R
R/get_plink_download_url_linux.R
R/get_plink_download_url_mac.R
R/get_plink_download_url_win.R
R/get_plink_example_filename.R
R/get_plink_example_filenames.R
R/get_plink_exe_name.R
R/get_plink_folder.R
R/get_plink_help_text.R
R/get_plink_subfolder_name.R
R/get_plink_tutorial_data_filenames.R
R/get_plink_version.R
R/get_plink_versions.R
R/get_plink_zip_path.R
R/get_plinkr_filename.R
R/get_plinkr_filenames.R
R/get_plinkr_folder.R
R/get_plinkr_tempfilename.R
R/get_sample_ids_from_fam_file.R
R/get_sample_ids_from_fam_table.R
R/get_sample_ids_from_phe_file.R
R/get_sample_ids_from_phe_table.R
R/get_test_bed_table.R
R/get_test_bim_table.R
R/get_test_eigenval_table.R
R/get_test_eigenvec_table.R
R/get_test_fam_table.R
R/get_test_map_table.R
R/get_test_ped_table.R
R/get_test_pgen_table.R
R/get_test_phe_table.R
R/get_test_psam_table.R
R/get_test_pvar_table.R
R/get_test_sample_ids.R
R/has_bed_table_attributes.R
R/has_pgen_table_attributes.R
R/has_plink2_bin_files.R
R/has_plink_bin_files.R
R/has_plink_text_files.R
R/install_plink.R
R/install_plink_tutorial_data.R
R/install_plinks.R
R/is_assoc_qt_data.R
R/is_bed_table.R
R/is_bim_table.R
R/is_chromosome_selector.R
R/is_data.R
R/is_exe.R
R/is_fam_table.R
R/is_map_table.R
R/is_marees_et_al_data_installed.R
R/is_on_ci.R
R/is_one_trait.R
R/is_ped_table.R
R/is_pgen_table.R
R/is_phenotype_data_filename.R
R/is_phenotype_data_table.R
R/is_plink2_bin_data.R
R/is_plink2_bin_filenames.R
R/is_plink_bin_data.R
R/is_plink_bin_filenames.R
R/is_plink_installed.R
R/is_plink_text_data.R
R/is_plink_text_filenames.R
R/is_plink_tutorial_data_installed.R
R/is_psam_table.R
R/is_pvar_table.R
R/is_random_samples_selector.R
R/is_random_snps_selector.R
R/is_sample_selector.R
R/is_single_sample_selector.R
R/is_single_snp_selector.R
R/is_snp_range_selector.R
R/is_snp_selector.R
R/is_snp_window_selector.R
R/keep.R
R/make_bed.R
R/make_bed_with_plink.R
R/make_bed_with_plink2.R
R/make_pgen.R
R/missing.R
R/missing_from_bfiles.R
R/pca.R
R/plink2_assoc.R
R/plink2_assoc_on_plink2_bin_data.R
R/plink2_assoc_on_plink2_bin_files.R
R/plink_assoc.R
R/plinkr.R
R/plinkr_report.R
R/plot_pca_results.R
R/read_plink2_bin_data.R
R/read_plink2_pgen_file.R
R/read_plink2_pgen_file_from_files.R
R/read_plink2_psam_file.R
R/read_plink2_pvar_file.R
R/read_plink2_qassoc_file.R
R/read_plink2_qassoc_files.R
R/read_plink_assoc_adjusted_file.R
R/read_plink_assoc_file.R
R/read_plink_bed_file.R
R/read_plink_bed_file_from_files.R
R/read_plink_bim_file.R
R/read_plink_bin_data.R
R/read_plink_cov_file.R
R/read_plink_eigenval_file.R
R/read_plink_eigenvec_file.R
R/read_plink_fam_file.R
R/read_plink_frq_file.R
R/read_plink_frq_strat_file.R
R/read_plink_imiss_file.R
R/read_plink_ld_file.R
R/read_plink_lmiss_file.R
R/read_plink_log_file.R
R/read_plink_map_file.R
R/read_plink_ped_file.R
R/read_plink_phe_file.R
R/read_plink_qassoc_file.R
R/read_plink_qassoc_files.R
R/read_plink_simfreq_file.R
R/read_plink_text_data.R
R/rename_fids.R
R/rename_iids.R
R/run_plink.R
R/save_bed_table.R
R/save_bim_table.R
R/save_cov_table.R
R/save_fam_table.R
R/save_map_table.R
R/save_ped_table.R
R/save_pgen_table.R
R/save_phe_table.R
R/save_phenotype_data_table.R
R/save_plink2_bin_data.R
R/save_plink_bin_data.R
R/save_plink_text_data.R
R/save_psam_table.R
R/save_pvar_table.R
R/save_qassoc_table.R
R/save_sample_ids.R
R/save_simulate_qt_params.R
R/select_samples.R
R/select_snps.R
R/simulate_qt.R
R/uninstall_plink.R
R/uninstall_plink_tutorial_data.R
R/uninstall_plinks.R
README.Rmd
README.md
Singularity
doc/.gitignore
doc/codecov_badge_92.png
doc/faq.md
doc/gha_build_badge_pass.png
doc/install.md
doc/poster_sbw2021.md
doc/poster_sbw2021.odg
doc/poster_sbw2021.pdf
doc/use_cases.md
inst/extdata/.gitignore
inst/extdata/assoc.assoc.adjusted
inst/extdata/assoc.assoc_1_row.adjusted
inst/extdata/assoc_input.cov
inst/extdata/assoc_qt_on_plink2_bin_files.pgen
inst/extdata/assoc_qt_on_plink2_bin_files.phe
inst/extdata/assoc_qt_on_plink2_bin_files.psam
inst/extdata/assoc_qt_on_plink2_bin_files.pvar
inst/extdata/assoc_qt_output_1_snp.qassoc
inst/extdata/assoc_qt_output_1_snp_nas.qassoc
inst/extdata/big_random.bed
inst/extdata/big_random.bim
inst/extdata/big_random.fam
inst/extdata/big_random.map
inst/extdata/big_random.ped
inst/extdata/big_random.phe
inst/extdata/demo_assoc.bed
inst/extdata/demo_assoc.bim
inst/extdata/demo_assoc.fam
inst/extdata/demo_assoc.log
inst/extdata/demo_assoc.map
inst/extdata/demo_assoc.ped
inst/extdata/demo_assoc_qt.bed
inst/extdata/demo_assoc_qt.bim
inst/extdata/demo_assoc_qt.fam
inst/extdata/demo_assoc_qt.log
inst/extdata/demo_assoc_qt.map
inst/extdata/demo_assoc_qt.ped
inst/extdata/demo_assoc_qt.phe
inst/extdata/frq_within.frq.strat
inst/extdata/gcaer_issue_2_bin.bed
inst/extdata/gcaer_issue_2_bin.bim
inst/extdata/gcaer_issue_2_bin.fam
inst/extdata/gcaer_issue_2_text.map
inst/extdata/gcaer_issue_2_text.ped
inst/extdata/gcaer_issue_2_text.phe
inst/extdata/miss_stat.frq
inst/extdata/miss_stat.frq.strat
inst/extdata/miss_stat.imiss
inst/extdata/miss_stat.lmiss
inst/extdata/miss_stat.log
inst/extdata/output.bed
inst/extdata/output.bim
inst/extdata/output.fam
inst/extdata/output.log
inst/extdata/output_plink1.bed
inst/extdata/output_plink1.bim
inst/extdata/output_plink1.fam
inst/extdata/output_plink1.log
inst/extdata/pca.bed
inst/extdata/pca.bim
inst/extdata/pca.eigenval
inst/extdata/pca.eigenvec
inst/extdata/pca.fam
inst/extdata/pca.log
inst/extdata/pheno.raw
inst/extdata/pheno_with_custom_header.phe
inst/extdata/pheno_with_header.phe
inst/extdata/pheno_with_standard_header.phe
inst/extdata/plink.log
inst/extdata/plink.simfreq
inst/extdata/plink2_assoc_output.additive.glm.linear
inst/extdata/plink2_assoc_output.log
inst/extdata/plink2_assoc_output.random.glm.linear
inst/extdata/qassoc_output_with_nan.qassoc
inst/extdata/random.map
inst/extdata/run1.assoc
inst/extdata/run1.qassoc
inst/extdata/select_snps.bed
inst/extdata/select_snps.bim
inst/extdata/select_snps.fam
inst/extdata/select_snps.phe
inst/extdata/select_snps_labels.csv
inst/extdata/select_snps_plink2.log
inst/extdata/select_snps_plink2.pgen
inst/extdata/select_snps_plink2.psam
inst/extdata/select_snps_plink2.pvar
inst/extdata/test_v1_7.map
inst/extdata/test_v1_7.ped
inst/extdata/test_v1_7_after_make-bed.bed
inst/extdata/test_v1_7_after_make-bed.bim
inst/extdata/test_v1_7_after_make-bed.fam
inst/extdata/test_v1_7_after_make-bed.log
inst/extdata/test_v1_7_after_make-bed_after_make-pgen.log
inst/extdata/test_v1_7_after_make-bed_after_make-pgen.pgen
inst/extdata/test_v1_7_after_make-bed_after_make-pgen.psam
inst/extdata/test_v1_7_after_make-bed_after_make-pgen.pvar
inst/extdata/toy_95.map
inst/extdata/toy_96.map
inst/extdata/toy_data.bed
inst/extdata/toy_data.bim
inst/extdata/toy_data.fam
inst/extdata/toy_data.frq
inst/extdata/toy_data.log
inst/extdata/toy_v1_9.map
inst/extdata/toy_v1_9.ped
inst/extdata/toy_v1_9_after_make-bed.bed
inst/extdata/toy_v1_9_after_make-bed.bim
inst/extdata/toy_v1_9_after_make-bed.fam
inst/extdata/toy_v1_9_after_make-bed.log
inst/extdata/toy_v1_9_after_make-bed_after_make-pgen.pgen
inst/extdata/toy_v1_9_after_make-bed_after_make-pgen.psam
inst/extdata/toy_v1_9_after_make-bed_after_make-pgen.pvar
man/assoc.Rd
man/assoc_adjust_from_bfile.Rd
man/assoc_from_bfile.Rd
man/assoc_qt.Rd
man/assoc_qt_covar.Rd
man/assoc_qt_on_plink2_bin_data.Rd
man/assoc_qt_on_plink2_bin_files.Rd
man/assoc_qt_on_plink_bin_data.Rd
man/assoc_qt_on_plink_bin_files.Rd
man/assoc_qt_on_plink_text_data.Rd
man/assoc_qt_on_plink_text_files.Rd
man/calc_additive_phenotype_values.Rd
man/calc_dominant_phenotype_values.Rd
man/calc_epistatic_phenotype_values.Rd
man/calc_random_case_control_phenotype_values.Rd
man/calc_random_phenotype_values.Rd
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