| .onAttach |
Source code
|
| .onLoad |
Source code
|
| GWASinspector |
Man page
|
| GWASinspector-package |
Man page
|
| Inspector |
Man page
|
| Inspector-class |
Man page
|
| QQ_plots |
Source code
|
| Study |
Man page
|
| Study-class |
Man page
|
| StudyList |
Man page
|
| StudyList-class |
Man page
|
| add_hIDcolumn |
Source code
|
| applyHQfilter |
Source code
|
| calculateKurtosis |
Source code
|
| calculateKurtosis_HQ |
Source code
|
| calculateLambda |
Source code
|
| calculatePercent |
Source code
|
| calculatePlotThreshold |
Source code
|
| calculateSkewness |
Source code
|
| calculateSkewness_HQ |
Source code
|
| calculateVischerStats |
Source code
|
| calculateVischerStats_HQ |
Source code
|
| calculate_PVALUE |
Source code
|
| calculate_af_correlation_alt_ref |
Source code
|
| calculate_af_correlation_std_ref |
Source code
|
| calculate_pvalue_correlation |
Source code
|
| changeColumnNameGCTA |
Source code
|
| changeColumnNameGWAMA |
Source code
|
| changeColumnNameGenABEL |
Source code
|
| changeColumnNameMETA |
Source code
|
| changeColumnNamePLINK |
Source code
|
| changeColumnNames |
Source code
|
| changeColumnOrder |
Source code
|
| changeROptions |
Source code
|
| checkAltReferenceFileIntegrity |
Source code
|
| checkBetaReferenceFileIntegrity |
Source code
|
| checkConfigFile |
Source code
|
| checkConfigFileSections |
Source code
|
| checkConfigParameters |
Source code
|
| checkDuplicatedHID_in_Alt_Ref |
Source code
|
| checkFolderPermission |
Source code
|
| checkReferenceFileIntegrity |
Source code
|
| checkRequiredColumnNames |
Source code
|
| check_awk |
Source code
|
| check_diffEAF |
Source code
|
| check_each_GWAS_file |
Source code
|
| check_ggplot2_version |
Source code
|
| check_gzip |
Source code
|
| check_if_files_exist_and_more_than_one |
Source code
|
| check_java |
Source code
|
| check_kableExtra_package |
Source code
|
| check_output_dir |
Source code
|
| check_output_report_files |
Source code
|
| check_pandoc |
Source code
|
| check_rJava_package |
Source code
|
| check_rsqlite_package |
Source code
|
| check_tools |
Source code
|
| check_unzip |
Source code
|
| check_wc |
Source code
|
| check_xlsx_package |
Source code
|
| clean_multi_alleles |
Source code
|
| compareInputfileWithAlternateReferenceFile |
Source code
|
| compareInputfileWithBetaReferenceFile |
Source code
|
| compareInputfileWithReferenceData |
Source code
|
| compareInputfileWithReferenceDataBase |
Source code
|
| compareInputfileWithReferenceFile |
Source code
|
| compareInputfileWithStoredReferenceFile |
Source code
|
| compare_GWASs |
Man page
Source code
|
| correct_extreme_calculated_pvalues |
Source code
|
| correct_extreme_pvalues |
Source code
|
| count_NA |
Source code
|
| create_Study |
Source code
|
| create_comparison_plots |
Source code
|
| create_file_specific_config |
Source code
|
| create_report_files |
Source code
|
| create_xlsx_report |
Source code
|
| deconvert_column_CHR |
Source code
|
| demo_inspector |
Man page
Source code
|
| drawPlots |
Source code
|
| effect_size_ref_make |
Source code
|
| evaluateListsAsStrings |
Source code
|
| example_config |
Source code
|
| file_excel_sheet |
Source code
|
| fill_missing_chr_positions |
Source code
|
| fill_missing_pvalues_from_calculated_pvalues |
Source code
|
| finalReport_to_txt_file |
Source code
|
| find_and_remove_ChromosomeVariant |
Source code
|
| first_excel_sheet |
Source code
|
| generateEffectSizePlot |
Source code
|
| getCrucialColumnNames_onFileAnalysis |
Source code
|
| getCrucialColumnNames_onFileLoading |
Source code
|
| getDefaultSystemOptions |
Source code
Source code
|
| getFileHeaderKV |
Source code
|
| getMultiAlleleCountTbl |
Source code
|
| getNonCrucialColumnNames |
Source code
|
| getRSQLiteDatabase |
Source code
|
| getRSQLiteDatabase_SubPopulationExists |
Source code
|
| getRSQLiteDatabase_hasINDEL |
Source code
|
| getRSQLiteDatabase_tableCount |
Source code
|
| getRSQLiteDatabase_tableNames |
Source code
|
| getRequiredColumnNames |
Source code
|
| get_OS |
Source code
|
| get_R_version |
Source code
|
| get_config |
Man page
Source code
|
| get_file_line_count |
Source code
|
| get_file_line_count_RUtils |
Source code
|
| get_headerTranslation |
Man page
Source code
|
| get_multi_file_report_template |
Source code
|
| get_precision_plot_values |
Source code
|
| get_skewness_kurtosis |
Source code
|
| get_study_name |
Source code
|
| get_study_specific_report_template |
Source code
|
| increment |
Source code
|
| input_data_preAnalysis_report |
Source code
|
| input_data_preprocessing |
Source code
|
| is_empty |
Source code
|
| make_config |
Source code
|
| man_plot |
Source code
|
| manhattan_plot |
Man page
Source code
|
| merge_rs |
Source code
|
| multi_file_comparison |
Source code
|
| multi_file_html_report_file |
Source code
|
| multi_file_txt_report_file |
Source code
|
| multi_study_eff_plot |
Source code
|
| multi_study_precision_plot |
Source code
|
| multi_study_skew_kurt_plot |
Source code
|
| plotScatterSmooth_DataMAF_vs_RefMAF |
Source code
|
| plotScatterSmooth_observedP_vs_expectedP |
Source code
|
| plot_DataEFFECT_vs_RefEFFECT |
Source code
|
| plot_DataMAF_vs_RefMAF |
Source code
|
| plot_manhattan_standalone |
Source code
|
| plot_observedP_vs_expectedP |
Source code
|
| plot_observedP_vs_expectedP_dual |
Source code
|
| plot_qqplot_af |
Source code
|
| plot_qqplot_call |
Source code
|
| plot_qqplot_hwe |
Source code
|
| plot_qqplot_impq |
Source code
|
| plot_variable_frequency_histograms |
Source code
|
| printConfigVariables |
Source code
|
| print_and_log |
Source code
|
| processCrucialColumns |
Source code
|
| processInputFile |
Source code
|
| processNonCrucialColumns |
Source code
|
| process_column_BOTH_ALL |
Source code
|
| process_column_CALLRATE |
Source code
|
| process_column_CHR |
Source code
|
| process_column_EFFECT |
Source code
|
| process_column_EFFECT_ALL |
Source code
|
| process_column_EFF_ALL_FREQ |
Source code
|
| process_column_HWE_PVAL |
Source code
|
| process_column_IMPUTED |
Source code
|
| process_column_IMP_QUALITY |
Source code
|
| process_column_MARKER |
Source code
|
| process_column_N_CASES |
Source code
|
| process_column_N_TOTAL |
Source code
|
| process_column_OTHER_ALL |
Source code
|
| process_column_POSITION |
Source code
|
| process_column_PVALUE |
Source code
|
| process_column_STDERR |
Source code
|
| process_column_STRAND |
Source code
|
| process_each_file |
Source code
|
| process_matched_data |
Source code
|
| reformat_columns |
Source code
|
| removeChromosomeVariants |
Source code
|
| removeDuplicateVariants |
Source code
|
| removeDuplicateVariants_postMatching |
Source code
|
| removeDuplicatedINDELs |
Source code
|
| removeDuplicatedLines |
Source code
|
| removeFunctionVariablesFromRAM |
Source code
|
| removeMonomorphicVariants |
Source code
|
| removeRedundantPlotFile |
Source code
|
| replaceInputStringFromHashSet |
Source code
|
| replaceInputStringSetFromHashSet |
Source code
|
| reportAlleleMatchStat |
Source code
|
| report_to_txt_file |
Source code
|
| resetDefaultSystemOptions |
Source code
Source code
|
| result_inspector |
Man page
Source code
|
| runStopCommand |
Source code
|
| run_inspector |
Man page
Source code
|
| saveDataSet |
Source code
|
| saveDataSet_final |
Source code
|
| save_NA_Dataset |
Source code
|
| save_alternate_reference |
Source code
|
| save_and_remove_unusable_variants |
Source code
|
| save_pre_modification_file |
Source code
|
| save_rds_file |
Source code
|
| save_remove_ambiguous_variants |
Source code
|
| save_remove_mismatch_Variants |
Source code
|
| save_significant_variants |
Source code
|
| search_database |
Source code
|
| second_excel_sheet |
Source code
|
| setColumnClass |
Source code
|
| set_graphic_device |
Source code
|
| set_graphic_device_jpeg |
Source code
|
| set_graphic_device_png |
Source code
|
| set_graphic_device_tiff |
Source code
|
| set_test_run_variables |
Source code
|
| setupLogOptions |
Source code
|
| setup_inspector |
Man page
Source code
|
| switchNegativeStrandsToPositive |
Source code
|
| switch_allele |
Source code
|
| switch_allele_vectorized |
Source code
|
| switch_alleles_vectorized |
Source code
|
| switch_flip_variant |
Source code
|
| system_check |
Man page
Source code
|
| third_excel_sheet |
Source code
|
| thousand_sep |
Source code
|
| tri_to_bi_alleles |
Source code
|
| tri_to_bi_freq |
Source code
|
| update_alternate_reference |
Source code
|
| uploadAltReferenceFile |
Source code
|
| uploadBetaReferenceFile |
Source code
|
| uploadInputFile |
Source code
|
| uploadReferenceFile |
Source code
|
| validate_Inspector |
Source code
|
| variable_statistics_pre_matching |
Source code
|
| variantDiscrimination |
Source code
|
| variant_match |
Source code
|
| verify_files_with_user |
Source code
|
| writeExcelReportFile |
Source code
|
| writeFileComparisonTXTreport |
Source code
|
| writeMainReportFile |
Source code
|
| writeStudyReportFile |
Source code
|
| writeTXTreport |
Source code
|
| write_to_report_file |
Source code
|
