GWASinspector
Comprehensive and Easy to Use Quality Control of GWAS Results

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239
Source code
53
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13
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GWASinspector: Comprehensive and Easy to Use Quality Control of GWAS Results
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API

API for GWASinspector
Comprehensive and Easy to Use Quality Control of GWAS Results

Global functions
.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
cleanDirectoryName 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
convert_logP_to_P 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 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
GWASinspector documentation built on April 4, 2025, 4:35 a.m.

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