| assoc | Let 'PLINK'/'PLINK2' detect an association for a case/control... |
| assoc_adjust_from_bfile | Let 'PLINK'/'PLINK2' do a binary-trait/case-control... |
| assoc_from_bfile | Let 'PLINK'/'PLINK2' do a binary-trait/case-control... |
| assoc_qt | Let 'PLINK'/'PLINK2' detect an association with one or more... |
| assoc_qt_covar | Let PLINK detect an association with one ore more... |
| assoc_qt_on_plink2_bin_data | Let 'PLINK2' detect an association with one or more... |
| assoc_qt_on_plink2_bin_files | Let 'PLINK2' detect an association with one or more... |
| assoc_qt_on_plink_bin_data | Let PLINK detect an association with one or more quantitative... |
| assoc_qt_on_plink_bin_files | Let 'PLINK' detect an association with one or more... |
| assoc_qt_on_plink_text_data | Let PLINK detect an association with one or more quantitative... |
| assoc_qt_on_plink_text_files | Let 'PLINK' detect an association with one or more... |
| calc_additive_phenotype_values | Calculate the phenotypic values for a trait that is perfectly... |
| calc_dominant_phenotype_values | Calculate the phenotypic values for a trait that is dominant. |
| calc_epistatic_phenotype_values | Calculate the phenotypic values for a trait that is... |
| calc_random_case_control_phenotype_values | Calculate the phenotypic values for a case-control trait that... |
| calc_random_phenotype_values | Calculate the phenotypic values for a trait that is random. |
| calc_rnorm_phenotype_values | Calculate the phenotypic values for a trait that is random... |
| calc_runif_phenotype_values | Calculate the phenotypic values for a trait that is random... |
| can_plink_version_and_data_can_work_together | Determine if the 'data' and the version of 'PLINK'/'PLINK2'... |
| check_allow_no_sex | Check if the 'allow_no_sex' is valid. Check if the... |
| check_assoc_data | Check if the 'assoc_data' are valid |
| check_assoc_params | Check if the 'assoc_params' are valid, will stop otherwise |
| check_assoc_qt_covar_data | Check if the 'assoc_qt_covar_data' are valid, will stop... |
| check_assoc_qt_covar_params | Check if the 'assoc_qt_covar_params' are valid, will stop... |
| check_assoc_qt_data | Check if the 'assoc_qt_data' is valid |
| check_assoc_qt_params | Check if the 'assoc_qt_params' are valid, will stop otherwise |
| check_assoc_qt_result | Check if a 'assoc_qt_result' is valid. |
| check_assoc_table | Check if a '.assoc' table is valid. |
| check_base_input_filename | Check if the 'base_input_filename' is valid. Check if the... |
| check_base_output_filename | Check if the 'base_output_filename' is valid. Check if the... |
| check_bed_table | Check if a '.bed' table is valid. |
| check_bim_table | Check if a '.bim' table is valid. |
| check_calc_phenotype_function | Check if the 'calc_phenotype_function' is valid. Check if the... |
| check_chromosome_number | Check if the chromosome number is valid. Check if the... |
| check_chromosome_selector | Check if a chromosome selector is valid. |
| check_confidence_interval | Check if the 'confidence_interval' is valid. Check if the... |
| check_cov_table | Check if a covariate table is valid. |
| check_data | Check if the data is valid |
| check_empty_plinkr_folder | Check there are no files in the default plinkr folder |
| check_equal_number_of_snvs | Internal function |
| check_fam_filename | Checks that the 'fam_filename' is valid |
| check_fam_table | Check if a '.fam' table is valid. |
| check_fid | Check if a family ID is valid |
| check_fids | Check if one or more family IDs are valid |
| check_iid | Check if a within-family ID is valid |
| check_iids | Check if one or more within-family IDs are valid |
| check_ld_window_r2 | Check if the 'ld_window_r2' is valid. Check if the... |
| check_maf | Check if the 'maf' is valid. Check if the 'maf', an... |
| check_mafs | Check the 'mafs', the minor allele frequencies. |
| check_map_table | Check if a genetic mapping '.map' table is valid. |
| check_n_individuals | Check if the number of individual is valid. |
| check_n_samples | Check if the number of samples is valid. Check if the number... |
| check_n_snps | Check if the number of SNPs is valid. Check if the number of... |
| check_os | Checks if the operating system is supported |
| check_pca_result_filenames | Check if a 'pca_result_filenames' is valid. |
| check_ped_table | Check if a '.ped' table is valid. |
| check_pgen_table | Check if a '.pgen' table is valid. |
| check_phe_filename | Checks that the 'phe_filename' is valid |
| check_phe_file_ok_for_qt | Check if a phenotype files holds a table that is valid for... |
| check_phenotype_data | Check if the 'phenotype_data' is valid |
| check_phenotype_data_filename | Check if the 'phenotype_data_filename' is valid. |
| check_phenotype_data_table | Check if the 'phenotype_data_table' is valid. |
| check_phenotypes | Check if the phenotypes are indeed phenotypes with a clear... |
| check_phe_table | Check if a phenotype table is valid. |
| check_phe_table_ok_for_qt | Check if a phenotype table is valid for use in a quantitative... |
| check_plink2_bin_data | Check if the 'PLINK2' bin data is valid. |
| check_plink2_bin_filenames | Checks that the 'plink2_bin_filenames' is valid |
| check_plink_args | Check if the PLINK version is valid, will stop if not |
| check_plink_bin_data | Check if the 'PLINK' bin data is valid. |
| check_plink_bin_filenames | Checks that the 'plink_bin_filenames' is valid |
| check_plink_filenames | Check if a 'plink_filenames' is valid. |
| check_plink_is_installed | Check if PLINK is installed |
| check_plink_options | Check if the options to run PLINK are valid. |
| check_plink_optionses | Check if the multiple sets of options to run PLINK are valid. |
| check_plink_text_data | Check if the 'PLINK' text data is valid. |
| check_plink_text_filenames | Checks that the 'plink_text_filenames' is valid |
| check_plink_version | Check if the PLINK version is valid, will stop if not |
| check_plink_version_and_data_can_work_together | Internal function to check if the 'PLINK'/'PLINK2' version... |
| check_psam_table | Check if a '.psam' table is valid. |
| check_pvar_table | Check if a '.pvar' table is valid. |
| check_qassoc_table | Check if a 'qassoc_table' is valid. |
| check_random_samples_selector | Check if a random-sample selector is valid. |
| check_random_snps_selector | Check if a random-SNP selector is valid. |
| check_sample_ids | Check if a 'sample_ids' is valid. |
| check_sample_ids_filename | Checks that the 'sample_ids_filename' is valid |
| check_sample_selector | Check if sample selector is valid. |
| check_simulate_qt_params | Check if the input is a valid set of parameters to simulate a... |
| check_single_sample_selector | Check if a single-sample selector is valid. |
| check_single_snp_selector | Check if a single-SNP selector is valid. |
| check_snp | Checks that the 'snp' is valid |
| check_snp_range_selector | Check if a SNP range selector is valid. |
| check_snp_selector | Check if SNP selector is valid. |
| check_snp_window_selector | Check if SNP windows selector is valid. |
| check_snvs | Check the single nucleotide variations. |
| check_trait | Check if a trait is valid. |
| check_traits | Check if a list of traits is valid. |
| check_verbose | Check if the 'verbose' is valid. Check if the 'verbose' is... |
| check_window_kb | Check if the window size (in kilobases) is valid. Check if... |
| clear_plink_folder | Deletes all files in the default 'PLINK' folder |
| clear_plinkr_cache | Clear the plinkr cache |
| compare_assoc_qt_speed | Compare speed when using assoc_qt for one 'assoc_qt_params'... |
| convert_bed_table_to_pgen_table | Convert a 'PLINK' '.bed' table to a 'PLINK2' '.pgen' table |
| convert_bim_table_to_map_table | Convert a 'PLINK' '.bim' table to a 'PLINK' '.map' table |
| convert_pgen_table_to_bed_table | Convert a 'PLINK2' '.pgen' table to a 'PLINK' '.bed' table |
| convert_plink2_bin_data_to_plink_bin_data | Convert the 'PLINK2' binary data to 'PLINK' binary data |
| convert_plink2_bin_data_to_plink_text_data | Convert the 'PLINK2' binary data to 'PLINK' binary data |
| convert_plink2_bin_files_to_plink_bin_files | Convert 'PLINK2' binary data files to 'PLINK' binary data... |
| convert_plink2_bin_files_to_plink_text_files | Convert 'PLINK2' binary data files to 'PLINK' text data files |
| convert_plink_bin_data_to_ped_table | Convert 'PLINK' binary data to a 'PLINK' '.ped' table |
| convert_plink_bin_data_to_plink2_bin_data | Convert the 'PLINK' binary data to 'PLINK2' binary data |
| convert_plink_bin_data_to_plink_text_data | Convert the 'PLINK' binary data to 'PLINK' text data |
| convert_plink_bin_files_to_plink2_bin_files | Convert 'PLINK' binary data files to 'PLINK2' binary data... |
| convert_plink_bin_files_to_plink_text_files | Convert PLINK binary files to PLINK plain-text files |
| convert_plink_bin_files_to_plink_vcf_files | Convert PLINK binary files to PLINK VCF files |
| convert_plink_text_data_to_plink2_bin_data | Convert the 'PLINK' text data to 'PLINK' binary data |
| convert_plink_text_data_to_plink_bin_data | Convert the 'PLINK' text data to 'PLINK' binary data |
| convert_plink_text_files_to_plink2_bin_files | Convert 'PLINK' text data files to 'PLINK2' binary data files |
| convert_plink_text_files_to_plink_bin_files | Convert 'PLINK' text files to 'PLINK' binary files |
| convert_psam_table_to_fam_table | Convert a 'PLINK2' '.psam' table to a 'PLINK' '.fam' table |
| convert_pvar_table_to_bim_table | Convert a 'PLINK2' '.pvar' table to a 'PLINK' '.bim' table |
| create_additive_trait | Create a trait in which the phenotype is additive and the... |
| create_assoc_args | Create the command-line arguments to call PLINK or PLINK2 |
| create_assoc_data | Create data for the assoc function |
| create_assoc_params | Create parameters for the assoc function |
| create_assoc_qt_args | Create the command-line arguments to call 'PLINK' or 'PLINK2'... |
| create_assoc_qt_args_on_plink2_bin_data | Internal function |
| create_assoc_qt_args_on_plink2_bin_filenames | Internal function |
| create_assoc_qt_args_on_plink_bin_data | Internal function |
| create_assoc_qt_args_on_plink_bin_filenames | Internal function |
| create_assoc_qt_args_on_plink_text_data | Internal function |
| create_assoc_qt_args_on_plink_text_filenames | Internal function |
| create_assoc_qt_covar_args | Create the command-line arguments to call 'PLINK' or 'PLINK2'... |
| create_assoc_qt_covar_data | Create data for the assoc_qt_covar function |
| create_assoc_qt_covar_params | Create parameters for the assoc_qt_covar function |
| create_assoc_qt_data | Create the data needed for the assoc_qt function |
| create_assoc_qt_params | Create parameters for the assoc_qt function |
| create_bgen_files_for_saige | Create the '.bgen' files for 'SAIGE' |
| create_chromosome_selector | Create a selector to select all SNPs on a chromosome |
| create_convert_plink_bin_files_to_plink_text_files_args | Create the command-line arguments to convert PLINK binary... |
| create_cov_table_from_data | Create a single-covariate table from pedigree ('.ped') table |
| create_cov_table_from_ped_table | Create a single-covariate table from pedigree ('.ped') table |
| create_custom_plink_options | Create the options to run a custom PLINK version |
| create_custom_trait | Create a custom trait in which the phenotype is determined in... |
| create_demo_assoc_data | Create a set of 'assoc' parameters to demonstrate PLINKs... |
| create_demo_assoc_qt_covar_data | Create a set of 'assoc_qt_covar' parameters to demonstrate... |
| create_demo_assoc_qt_data | Create a set of assoc_qt data to demonstrate PLINKs... |
| create_demo_map_table | Create a demo genetic mapping '.map' table |
| create_demo_ped_table | Create a demo pedigree '.ped' table |
| create_demo_ped_table_lhs | Internal function |
| create_demo_ped_table_rhs | Internal function |
| create_demo_ped_table_rhs_trait | Internal function |
| create_demo_phe_table | Create a demo phenotype table |
| create_demo_phe_table_lhs | Internal function |
| create_demo_phe_table_rhs | Internal function |
| create_demo_traits | Create some traits with a clear genetic architecture and a... |
| create_dominant_trait | Create a trait in which the phenotype is dominant and the... |
| create_epistatic_trait | Create a trait in which the phenotype is epistatic and the... |
| create_keep_args | Create the CLI arguments to call 'PLINK' with the '–keep'... |
| create_pca_args | Create the CLI arguments to call 'PLINK' with the '–pca'... |
| create_phenotype_data_filename | Create a 'phenotype_data_filename' |
| create_phenotype_data_table | Create a 'phenotype_data_table' |
| create_phenotype_data_table_from_data | Create a 'phenotype_data' from the PLINK data. |
| create_phe_table_from_data | Create a single-phenotype table from the PLINK data. |
| create_phe_table_from_fam_table | Create a single-phenotype table from pedigree ('.fam') table |
| create_phe_table_from_ped_table | Create a single-phenotype table from pedigree ('.ped') table |
| create_phe_table_from_plink2_bin_data | Create a single-phenotype table from a table within the... |
| create_phe_table_from_plink_bin2_filenames | Create a single-phenotype table from a table from the PLINK2... |
| create_phe_table_from_plink_bin_data | Create a single-phenotype table from the gentic mapping... |
| create_phe_table_from_plink_bin_filenames | Create a single-phenotype table from the data within the... |
| create_phe_table_from_plink_text_data | Create a single-phenotype table from pedigree ('.ped') table... |
| create_phe_table_from_plink_text_filenames | Create a single-phenotype table from pedigree ('.ped') table... |
| create_phe_table_from_psam_table | Create a single-phenotype table from pedigree ('.psam') table |
| create_plink2_bin_data | Create a set of 'PLINK2' binary data |
| create_plink2_bin_filenames | Create a 'plink2_bin_filenames' |
| create_plink_bin_data | Create a set of 'PLINK' binary data |
| create_plink_bin_filenames | Create a 'plink_bin_filenames' |
| create_plink_options | Create the options to run PLINK |
| create_plink_optionses | Create the PLINK options for all supported versions of PLINK |
| create_plink_text_data | Create a set of 'PLINK' textual data |
| create_plink_text_filenames | Create a 'plink_text_filenames' |
| create_plink_v1_7_options | Create the options to run PLINK v1.7 |
| create_plink_v1_9_options | Create the options to run PLINK v1.9 |
| create_plink_v2_0_options | Create the options to run PLINK v2.0 |
| create_random_case_control_trait | Create a case-control trait with no relation between genotype... |
| create_random_samples_selector | Create a random samples selector |
| create_random_snps_selector | Create a random SNP selector |
| create_random_trait | Create a trait with no relation between genotype and... |
| create_rnorm_trait | Create a trait with no relation between genotype and a... |
| create_runif_trait | Create a trait with no relation between genotype and a... |
| create_samples_selector | Create a sample selector |
| create_select_chromosome_args | Create the command-line arguments to select a chromosome |
| create_selected_sample_ids | Create a table of the selected sample IDs |
| create_select_random_samples_args | Create the command-line arguments to select random samples |
| create_select_random_snp_args | Create the command-line arguments to select a range SNPs |
| create_select_samples_args | Create the command-line arguments to select samples |
| create_select_single_sample_args | Create the command-line arguments to select a single sample |
| create_select_single_snp_args | Create the command-line arguments to select a single SNP |
| create_select_snp_range_args | Create the command-line arguments to select a range SNPs |
| create_select_snps_args | Create the command-line arguments to select SNPs |
| create_select_snp_window_args | Create the command-line arguments to select SNPs |
| create_simulate_qt_params | Create a set of parameters for simulating a quantitative... |
| create_single_sample_selector | Create a sample selector to select a single sample |
| create_single_snp_selector | Create a SNP selector to select a single SNP |
| create_snp_range_selector | Create a SNP range selector |
| create_snps_selector | Create a SNP selector |
| create_snp_window_selector | Create a SNP window selector |
| create_snvs | Create a table with single nucleotide variants (SNVs) |
| create_test_assoc_data | Create testing data for the assoc function |
| create_test_assoc_params | Create testing parameters for the assoc function |
| create_test_assoc_qt_covar_data | Create a dataset for the assoc_qt function to be used in... |
| create_test_assoc_qt_covar_params | Create parameters for the assoc_qt_covar function to be used... |
| create_test_assoc_qt_data | Create testing data for the assoc_qt function |
| create_test_assoc_qt_params | Create testing parameters for the assoc_qt function |
| create_test_chromosome_selector | Create a selector to select all SNPs on a chromosome, to be... |
| create_test_pca_result_filenames | Create a 'pca_result_filenames' to be used in testing. |
| create_test_phenotype_data_filename | Create a 'phenotype_data_filename' to be used in testing |
| create_test_phenotype_data_table | Create a 'phenotype_data_table' to be used in testing |
| create_test_plink2_bin_data | Create a set of 'PLINK2' binary data to be used in testing |
| create_test_plink2_bin_filenames | Create a 'plink2_bin_filenames' to be used in testing. |
| create_test_plink_bin_data | Create a set of 'PLINK' binary data to be used in testing |
| create_test_plink_bin_filenames | Create a set of 'plink_bin_filenames' to be used in testing. |
| create_test_plink_text_data | Create PLINK text data for testing |
| create_test_plink_text_filenames | Create a set of 'plink_text_filenames' to be used in testing. |
| create_test_random_samples_selector | Create a random sample selector to be used in testing |
| create_test_random_snps_selector | Create a random SNP selector to be used in testing |
| create_test_simulate_qt_params | Create a set of testing parameters for simulating a... |
| create_test_single_sample_selector | Create a sample selector to select a single sample, to be... |
| create_test_single_snp_selector | Create a SNP selector to select a single SNP, to be used in... |
| create_test_snp_range_selector | Create a SNP range selector |
| create_test_snp_window_selector | Create a SNP window selector |
| create_trait | Create a trait with a clear genetic architecture and a known... |
| default_params_doc | This function does nothing. It is intended to inherit is... |
| do_plink_self_test | Do a minimal PLINK self test |
| filter_random_snps | Create a 'PLINK' dataset that has randomly selected SNPs |
| freq_from_bfile | Let 'PLINK'/'PLINK2' calculate the allele frequencies. |
| freq_from_bfile_within_phe_file | Let 'PLINK'/'PLINK2' calculate the allele frequencies per... |
| get_data_description | Get a description of the data |
| get_default_plink_exe_path | Get the path to the default PLINK executable as used by... |
| get_default_plink_version | Get the default PLINK version as used by plinkr |
| get_heighest_maf | Get the highest value for a minor allelle frequency (MAF). |
| get_lowest_maf | Get the lowest non-zero value for a minor allelle frequency... |
| get_marker_correlation_coefficients | Get the marker correlation coefficients (also known as 'r')... |
| get_marker_correlation_coefficients_table | Get the marker correlation coefficients (also known as 'r')... |
| get_minor_alelle_frequencies | Get the minor allele frequencies from genetic data |
| get_n_samples | Get the number of samples from a table |
| get_n_samples_from_bed_table | Get the number of samples from a '.bed' table |
| get_n_samples_from_bim_table | Get the number of samples from a '.bim' table |
| get_n_samples_from_fam_table | Get the number of samples from a '.fam' table |
| get_n_samples_from_map_table | Get the number of samples from a '.map' table |
| get_n_samples_from_ped_table | Get the number of samples from a '.ped' table |
| get_n_samples_from_pgen_table | Get the number of samples from a '.pgen' table |
| get_n_samples_from_psam_table | Get the number of samples from a '.psam' table |
| get_n_samples_from_pvar_table | Get the number of samples from a '.pvar' table |
| get_n_snps | Get the number of SNPs from a table |
| get_n_snps_from_bed_table | Get the number of SNPs from a '.bed' table |
| get_n_snps_from_bim_table | Get the number of SNPs from a '.bim' table |
| get_n_snps_from_map_table | Get the number of SNPs from a '.map' table |
| get_n_snps_from_ped_table | Get the number of SNPs from a '.ped' table |
| get_n_snps_from_pgen_table | Get the number of SNPs from a '.pgen' table |
| get_n_snps_from_pvar_table | Get the number of SNPs from a '.pvar' table |
| get_os | Get the current operating system |
| get_phenotypes | Get the phenotypes that are named after their genetic... |
| get_plink1_versions | Get the supported version of PLINK |
| get_plink2_versions | Get the supported version of PLINK2 |
| get_plink_download_url | Get the URL to download a version of PLINK from |
| get_plink_download_url_linux | Get the URL to download a Linux version of PLINK |
| get_plink_download_url_mac | Get the URL to download a Mac version of PLINK |
| get_plink_download_url_win | Get the URL to download a 64-bit Windows version of PLINK |
| get_plink_example_filename | Get the path to a PLINK example file |
| get_plink_example_filenames | Get the full paths to all PLINK example files |
| get_plink_exe_name | Get the name of the PLINK executable |
| get_plink_folder | Get the path to the default 'PLINK' folder as used by plinkr |
| get_plink_help_text | Get the text of the PLINK help file |
| get_plinkr_filename | Get the path to a plinkr file |
| get_plinkr_filenames | Get the full paths to all plinkr files |
| get_plinkr_folder | Get the folder where plinkr stores its temporary files |
| get_plinkr_tempfilename | Get a temporary filename |
| get_plink_subfolder_name | Get the path to the default 'PLINK' subfolder as used by... |
| get_plink_tutorial_data_filenames | Install the 'PLINK' tutorial data |
| get_plink_version | Get the version of PLINK |
| get_plink_versions | Get the supported version of PLINK and PLINK2 |
| get_plink_zip_path | Get the path to the default 'PLINK' executable as used by... |
| get_sample_ids_from_fam_file | Get the sample IDs from a 'fam' file |
| get_sample_ids_from_fam_table | Get the sample IDs from a '.fam' file |
| get_sample_ids_from_phe_file | Get the sample IDs from a '.phe' file |
| get_sample_ids_from_phe_table | Get the sample IDs from a '.phe' file |
| get_test_bed_table | Get a simple '.bed' table |
| get_test_bim_table | Get a simple genetic mapping ('.bim') table |
| get_test_eigenval_table | Get a simple '.eigenval' table |
| get_test_eigenvec_table | Get a simple '.eigenvec' table |
| get_test_fam_table | Get a simple ('.fam') table |
| get_test_map_table | Get a simple genetic mapping ('.map') table |
| get_test_ped_table | Get a simple pedigree ('.ped') table. |
| get_test_pgen_table | Get a simple '.pgen' table |
| get_test_phe_table | Create a phenotype table ('phe_table') to be used in testing |
| get_test_psam_table | Get a simple '.psam' table |
| get_test_pvar_table | Get a simple '.pvar' table |
| get_test_sample_ids | Create a 'sample_ids' to be used in testing |
| has_bed_table_attributes | Determine if the table has the attributes of a 'bed_table' |
| has_pgen_table_attributes | Determine if the table has the attributes of a 'pgen_table' |
| has_plink2_bin_files | Determine if using 'base_input_filename' there are 'PLINK'... |
| has_plink_bin_files | Determine if using 'base_input_filename' there are 'PLINK'... |
| has_plink_text_files | Determine if using 'base_input_filename' there are 'PLINK'... |
| install_plink | Install a specific version of PLINK |
| install_plinks | Install multiple versions of PLINK |
| install_plink_tutorial_data | Install the 'PLINK' tutorial data |
| is_assoc_qt_data | Determine if the 'assoc_qt_data' is indeed data used for a... |
| is_bed_table | Determine if a '.bed' table is valid. |
| is_bim_table | Determine if a '.bim' table is valid. |
| is_chromosome_selector | Determine if this is a chromosome selector |
| is_data | Determine if the 'data' is indeed 'PLINK' bin data |
| is_exe | Determine if a file can be executed |
| is_fam_table | Determine if a '.fam' table is valid. |
| is_map_table | Determine if a '.map' table is valid. |
| is_marees_et_al_data_installed | Determine if the tutorial data of Marees et al., 2018 is... |
| is_on_appveyor | Determines if the environment is AppVeyor |
| is_on_ci | Determines if the environment is a continuous integration... |
| is_one_trait | Determine if the input is one trait |
| is_on_github_actions | Determines if the environment is GitHub Actions |
| is_on_travis | Determines if the environment is Travis CI |
| is_ped_table | Determine if a '.ped' table is valid. |
| is_pgen_table | Determine if a '.pgen' table is valid. |
| is_phenotype_data_filename | Determine if the 'phenotype_data_filename' is indeed... |
| is_phenotype_data_table | Determine if the 'phenotype_data_table' is indeed phenotypic... |
| is_plink2_bin_data | Determine if the 'plink2_bin_data' is indeed 'PLINK2' binary... |
| is_plink2_bin_filenames | Determine if the 'plink2_bin_files' is indeed a set of... |
| is_plink_bin_data | Determine if the 'plink_bin_data' is indeed 'PLINK' bin data |
| is_plink_bin_filenames | Determine if the 'plink_bin_files' is indeed a set of 'PLINK'... |
| is_plink_installed | Determine if 'PLINK' is installed |
| is_plink_text_data | Determine if the 'plink_text_data' is indeed 'PLINK' text... |
| is_plink_text_filenames | Determine if the 'plink_text_files' is indeed a set of... |
| is_plink_tutorial_data_installed | Determine if the 'PLINK' tutorial data is installed. |
| is_psam_table | Determine if a '.pvar' table is valid. |
| is_pvar_table | Determine if a '.pvar' table is valid. |
| is_random_samples_selector | Determine if this is a random sample selector |
| is_random_snps_selector | Determine if this is a random SNPs selector |
| is_sample_selector | Determine if this is a sample selector |
| is_single_sample_selector | Determine if this is a single sample selector |
| is_single_snp_selector | Determine if this is a single SNP selector |
| is_snp_range_selector | Determine if this is a SNP range selector |
| is_snp_selector | Determine if this is a SNP selector |
| is_snp_window_selector | Determine if this is a SNP window selector |
| keep | Filter 'PLINK' and 'PLINK2' data on their family ID |
| make_bed | Convert to 'PLINK' binary files |
| make_bed_with_plink | Convert 'PLINK' text files to 'PLINK' binary files using... |
| make_bed_with_plink2 | Convert 'PLINK2' binary files to 'PLINK' binary files using... |
| make_pgen | Convert to 'PLINK2' binary files |
| missing_from_bfile | Let 'PLINK'/'PLINK2' calculate the missing rates summary... |
| pca | Do a principal component analysis |
| plink2_assoc | Let 'PLINK2' detect an association with one binary traits. |
| plink2_assoc_on_plink2_bin_data | Let 'PLINK2' detect an association with one binary trait on... |
| plink2_assoc_on_plink2_bin_files | Let 'PLINK2' detect an association with one binary trait on... |
| plink_assoc | Let PLINK detect an association with one binary traits. |
| plinkr | plinkr: An R interface to 'PLINK'. |
| plinkr_report | Create a plinkr report, to be used when reporting bugs |
| plot_pca_results | Plot the result of a call to pca |
| read_plink2_bin_data | Read 'PLINK2' binary files based on a shared base input... |
| read_plink2_pgen_file | Read a 'PLINK2' '.pgen' file |
| read_plink2_pgen_file_from_files | Read a 'PLINK2' '.pgen' file using a '.psam' and '.pvar'... |
| read_plink2_psam_file | Read a 'PLINK2' '.psam' file |
| read_plink2_pvar_file | Read a 'PLINK2' '.pvar' file |
| read_plink2_qassoc_file | Read a 'PLINK2' assoc_qt file |
| read_plink2_qassoc_files | Read one or more 'PLINK2' files that are created by assoc_qt |
| read_plink_assoc_adjusted_file | Read a PLINK '.assoc.adjusted' file |
| read_plink_assoc_file | Read a PLINK '.assoc' file |
| read_plink_bed_file | Read a 'PLINK'/'PLINK2' '.bed' file |
| read_plink_bed_file_from_files | Read a 'PLINK'/'PLINK2' '.bed' file using a '.bim' and '.fam'... |
| read_plink_bim_file | Read a 'PLINK'/'PLINK2' '.bim' file |
| read_plink_bin_data | Read 'PLINK' binary files based on a shared base input... |
| read_plink_cov_file | Read a 'PLINK' covariates file |
| read_plink_eigenval_file | Read a 'PLINK'/'PLINK2' '.eigenval' file |
| read_plink_eigenvec_file | Read a 'PLINK'/'PLINK2' '.eigenvec' file |
| read_plink_fam_file | Read a 'PLINK'/'PLINK2' '.fam' file |
| read_plink_frq_file | Read a PLINK '.frq' file |
| read_plink_frq_strat_file | Read a PLINK '.frq.strat' file |
| read_plink_imiss_file | Read a PLINK '.imiss' file |
| read_plink_ld_file | Read a PLINK '.ld' file |
| read_plink_lmiss_file | Read a PLINK '.lmiss' file |
| read_plink_log_file | Read a PLINK '.log' file |
| read_plink_map_file | Read a PLINK '.map' file |
| read_plink_ped_file | Read a PLINK '.ped' file |
| read_plink_phe_file | Read a 'PLINK' raw phenotype file |
| read_plink_qassoc_file | Read a PLINK '.qassoc' file |
| read_plink_qassoc_files | Read one or more 'PLINK' '.qassoc' file |
| read_plink_simfreq_file | Read a PLINK '.simfreq' file |
| read_plink_text_data | Read 'PLINK' text files based on a shared base input filename |
| rename_fids | Rename all the family IDs within the data |
| rename_iids | Rename all the within-family IDs within the data |
| run_plink | Run PLINK from arguments |
| save_bed_table | Save a '.bed' table to file. |
| save_bim_table | Save a '.bim' table to file. |
| save_cov_table | Save a '.cov' table to file |
| save_fam_table | Save a '.fam' table to file. |
| save_map_table | Save a '.map' table to file. |
| save_ped_table | Save a '.ped' table to file. |
| save_pgen_table | Save a '.pgen' table to file. |
| save_phenotype_data_table | Save a 'phenotype_data' (in the form of a... |
| save_phe_table | Save a '.phe' table to file |
| save_plink2_bin_data | Save 'PLINK2' binary data to files. |
| save_plink_bin_data | Save 'PLINK' binary data to files. |
| save_plink_text_data | Save 'PLINK' text data to files. |
| save_psam_table | Save a '.psam' table to file. |
| save_pvar_table | Save a '.pvar' table to file. |
| save_qassoc_table | Save a '.qassoc' table to file. |
| save_sample_ids | Save a 'sample_ids' to file. |
| save_simulate_qt_params | Save the parameters for a quantitative traits simulation to... |
| select_samples | Select samples/individuals |
| select_snps | Select SNPs |
| simulate_qt | Simulate a quantitative trait |
| uninstall_plink | Uninstall PLINK |
| uninstall_plinks | Uninstall multiple versions of PLINK |
| uninstall_plink_tutorial_data | Uninstall the 'PLINK' tutorial data |
