marvel API
This section documents the MARVELous Python API for programmatic usage.
marvel.pipelinemodulemarvel.associationpackagemarvel.extractionpackagemarvel.extraction.coremodulemarvel.extraction.extractionmodulemarvel.extraction.aggregationmodule
marvel.utilspackagemarvel.utils.config_toolsmoduleConfigParser()PipelineConfigPipelineConfig.alt_columnPipelineConfig.association_analysisPipelineConfig.cat_columnPipelineConfig.checkpoint_dirPipelineConfig.chr_columnPipelineConfig.chr_pos_columnPipelineConfig.cov_filePipelineConfig.cov_miss_errorPipelineConfig.covariate_modelsPipelineConfig.exp_filesPipelineConfig.exposuresPipelineConfig.extract_variantsPipelineConfig.file_sepPipelineConfig.force_rerunPipelineConfig.from_config_dict()PipelineConfig.geno_filesPipelineConfig.id_columnPipelineConfig.incl_varPipelineConfig.listwisePipelineConfig.max_missingnessPipelineConfig.min_group_sizePipelineConfig.n_jobsPipelineConfig.neg_genoPipelineConfig.outcomesPipelineConfig.output_pathPipelineConfig.pheno_filePipelineConfig.pos_columnPipelineConfig.prefilter_regionsPipelineConfig.raise_on_errorPipelineConfig.ref_columnPipelineConfig.regionPipelineConfig.reversePipelineConfig.stratify_modelsPipelineConfig.stratify_overallPipelineConfig.sum_genoPipelineConfig.tmp_dirPipelineConfig.validate()PipelineConfig.var_columnPipelineConfig.var_filesPipelineConfig.var_sepPipelineConfig.variant_output
check_config_file()cnf_extract_outcome_tests()cnf_extract_survival_tests()create_config()custom_config()update_config_file()
marvel.utils.data_managermodulemarvel.utils.missingnessmoduleMissingnessHandlerMissingnessHandler.filter_by_missingness()MissingnessHandler.get_complete_columns()MissingnessHandler.get_missing_summary()MissingnessHandler.get_valid_ids()MissingnessHandler.get_valid_ids_from_files()MissingnessHandler.handle()MissingnessHandler.handle_listwise()MissingnessHandler.handle_pairwise()
marvel.utils.utilsmodule