Index

A

add_inversed_column() (marvel.extraction.core.AlleleInverter method) aggregate() (marvel.extraction.aggregation.VariantToGeneAggregator method) AlleleComparator (class in marvel.extraction.core) AlleleInverter (class in marvel.extraction.core)

alt (marvel.extraction.core.Variant attribute) alt_column (marvel.utils.config_tools.PipelineConfig attribute) association_analysis (marvel.utils.config_tools.PipelineConfig attribute) AssociationResult (class in marvel.association.class_test) AssociationTestingStep (class in marvel.pipeline)

B

baseline_table (marvel.association.class_test.AssociationResult attribute)

BaselineTestWrapper (class in marvel.association.class_test) BgenReaderClass (class in marvel.extraction.extraction)

C

cat_column (marvel.utils.config_tools.PipelineConfig attribute) check_config_file() (in module marvel.utils.config_tools) check_environ() (in module marvel.utils.utils) check_extension() (in module marvel.utils.utils) check_sample_size() (marvel.association.class_test.DataValidator method) check_stratified_variation() (marvel.association.class_test.DataValidator method) check_string_columns() (marvel.association.class_test.DataValidator method) checkpoint_dir (marvel.utils.config_tools.PipelineConfig attribute) chr_column (marvel.utils.config_tools.PipelineConfig attribute) chr_pos_column (marvel.utils.config_tools.PipelineConfig attribute) chrom (marvel.extraction.core.Variant attribute) clear() (marvel.utils.data_manager.LRUCache method) clear_caches() (marvel.utils.data_manager.DataManager method)

cnf_extract_outcome_tests() (in module marvel.utils.config_tools) cnf_extract_survival_tests() (in module marvel.utils.config_tools) coefficient_table (marvel.association.class_test.AssociationResult attribute) compare() (marvel.extraction.core.AlleleComparator static method) ConfigParser() (in module marvel.utils.config_tools) count() (marvel.extraction.core.GenotypeCounter method) count_by_category() (marvel.extraction.core.GenotypeCounter method) count_gen() (in module marvel.extraction.core) cov_file (marvel.utils.config_tools.PipelineConfig attribute) cov_miss_error (marvel.utils.config_tools.PipelineConfig attribute) covariate_models (marvel.utils.config_tools.PipelineConfig attribute) create_config() (in module marvel.utils.config_tools) custom_config() (in module marvel.utils.config_tools)

D

DataManager (class in marvel.utils.data_manager)

DataValidator (class in marvel.association.class_test) DifferencesTester (class in marvel.association.class_test)

E

execute() (marvel.pipeline.AssociationTestingStep method) (marvel.pipeline.PipelineStep method) (marvel.pipeline.VariantExtractionStep method) execute_tasks() (marvel.extraction.extraction.VariantExtraction method) execute_tasks_parallel() (marvel.extraction.extraction.VariantExtraction method) exp_files (marvel.utils.config_tools.PipelineConfig attribute)

exposures (marvel.utils.config_tools.PipelineConfig attribute) extract() (marvel.extraction.aggregation.GeneExtractor method) (marvel.extraction.extraction.VariantExtractor method) extract_carriers() (in module marvel.extraction.extraction) extract_genes() (in module marvel.extraction.aggregation) extract_variants (marvel.utils.config_tools.PipelineConfig attribute) ExtractionTask (class in marvel.extraction.extraction)

F

file_sep (marvel.utils.config_tools.PipelineConfig attribute) filter_by_missingness() (marvel.utils.missingness.MissingnessHandler method)

force_rerun (marvel.utils.config_tools.PipelineConfig attribute) from_config_dict() (marvel.utils.config_tools.PipelineConfig class method) from_config_file() (marvel.pipeline.MARVELousPipeline class method)

G

GeneExtractor (class in marvel.extraction.aggregation) GeneticFileReader (class in marvel.extraction.extraction) geno_files (marvel.utils.config_tools.PipelineConfig attribute) geno_id (marvel.extraction.extraction.ExtractionTask attribute) geno_path (marvel.extraction.extraction.ExtractionTask attribute) GenotypeCounter (class in marvel.extraction.core) GenotypeProcessor (class in marvel.extraction.core) get() (marvel.utils.data_manager.LRUCache method) get_cache_stats() (marvel.utils.data_manager.DataManager method) get_complete_columns() (marvel.utils.missingness.MissingnessHandler method)

get_exposure() (marvel.utils.data_manager.DataManager method) get_merged_data() (marvel.utils.data_manager.DataManager method) get_missing_summary() (marvel.utils.missingness.MissingnessHandler method) get_regions() (marvel.extraction.extraction.BgenReaderClass method) (marvel.extraction.extraction.GeneticFileReader method) (marvel.extraction.extraction.PlinkReaderClass method) (marvel.extraction.extraction.VcfReaderClass method) get_summary() (marvel.pipeline.MARVELousPipeline method) get_valid_ids() (marvel.utils.missingness.MissingnessHandler method) get_valid_ids_from_files() (marvel.utils.missingness.MissingnessHandler method)

H

handle() (marvel.utils.missingness.MissingnessHandler method) handle_listwise() (marvel.utils.missingness.MissingnessHandler method)

handle_pairwise() (marvel.utils.missingness.MissingnessHandler method) has_rows() (in module marvel.utils.utils)

I

id_column (marvel.utils.config_tools.PipelineConfig attribute) identifier (marvel.extraction.extraction.ExtractionTask attribute) incl_var (marvel.utils.config_tools.PipelineConfig attribute)

infer_column_types() (in module marvel.utils.utils) InsufficientVariationError is_gzip() (in module marvel.utils.utils)

L

listwise (marvel.utils.config_tools.PipelineConfig attribute) load_covariates() (marvel.utils.data_manager.DataManager method) load_custom() (in module marvel.utils.utils) load_outcome() (marvel.utils.data_manager.DataManager method)

load_outcomes() (marvel.utils.data_manager.DataManager method) log_error() (marvel.pipeline.PipelineStep method) log_info() (marvel.pipeline.PipelineStep method) log_warning() (marvel.pipeline.PipelineStep method) LRUCache (class in marvel.utils.data_manager)

M

main() (in module marvel.marvelous_entry) marvel.association.class_test module marvel.extraction.aggregation module marvel.extraction.core module marvel.extraction.extraction module marvel.marvelous_entry module marvel.utils.config_tools module marvel.utils.data_manager module marvel.utils.missingness module marvel.utils.utils module

marvelous() (in module marvel.marvelous_entry) MARVELousPipeline (class in marvel.pipeline) max_missingness (marvel.utils.config_tools.PipelineConfig attribute) merge_dfs() (in module marvel.utils.utils) min_group_size (marvel.utils.config_tools.PipelineConfig attribute) MissingnessHandler (class in marvel.utils.missingness) ModelComparator (class in marvel.association.class_test) module marvel.association.class_test marvel.extraction.aggregation marvel.extraction.core marvel.extraction.extraction marvel.marvelous_entry marvel.utils.config_tools marvel.utils.data_manager marvel.utils.missingness marvel.utils.utils

N

n_jobs (marvel.utils.config_tools.PipelineConfig attribute)

neg_geno (marvel.utils.config_tools.PipelineConfig attribute)

O

open_file() (in module marvel.utils.utils) OutcomeCategoryTester (class in marvel.association.class_test)

outcomes (marvel.utils.config_tools.PipelineConfig attribute) output_path (marvel.utils.config_tools.PipelineConfig attribute)

P

pheno_file (marvel.utils.config_tools.PipelineConfig attribute) PipelineConfig (class in marvel.utils.config_tools) PipelineStep (class in marvel.pipeline) PlinkReaderClass (class in marvel.extraction.extraction) pos (marvel.extraction.core.Variant attribute)

pos_column (marvel.utils.config_tools.PipelineConfig attribute) prefilter_regions (marvel.utils.config_tools.PipelineConfig attribute) process() (marvel.extraction.core.VariantProcessor method) process_genotypes() (marvel.extraction.core.GenotypeProcessor static method) put() (marvel.utils.data_manager.LRUCache method)

Q

qc_dict() (in module marvel.utils.utils)

R

raise_on_error (marvel.utils.config_tools.PipelineConfig attribute) read() (marvel.extraction.extraction.BgenReaderClass method) (marvel.extraction.extraction.GeneticFileReader method) (marvel.extraction.extraction.PlinkReaderClass method) (marvel.extraction.extraction.VcfReaderClass method) read_if_new() (in module marvel.utils.utils) ref (marvel.extraction.core.Variant attribute) ref_column (marvel.utils.config_tools.PipelineConfig attribute) refactor_col() (in module marvel.utils.utils) region (marvel.utils.config_tools.PipelineConfig attribute)

reorder_alleles() (marvel.extraction.core.AlleleInverter method) resolve() (marvel.association.class_test.TestTypeResolver method) return_header_list() (in module marvel.utils.utils) reverse (marvel.utils.config_tools.PipelineConfig attribute) rsid (marvel.extraction.core.Variant attribute) run() (marvel.association.class_test.DifferencesTester method) (marvel.association.class_test.ModelComparator method) (marvel.association.class_test.OutcomeCategoryTester method) (marvel.pipeline.MARVELousPipeline method) run_single_test() (marvel.association.class_test.BaselineTestWrapper method)

S

sample_data (marvel.extraction.core.Variant attribute) set_exposure() (marvel.utils.data_manager.DataManager method) setup_tasks() (marvel.extraction.extraction.VariantExtraction method)

stratify_models (marvel.utils.config_tools.PipelineConfig attribute) stratify_overall (marvel.utils.config_tools.PipelineConfig attribute) sum_geno (marvel.utils.config_tools.PipelineConfig attribute)

T

TestTypeResolver (class in marvel.association.class_test)

tmp_dir (marvel.utils.config_tools.PipelineConfig attribute)

U

update_config_file() (in module marvel.utils.config_tools)

V

validate() (marvel.utils.config_tools.PipelineConfig method) var_column (marvel.utils.config_tools.PipelineConfig attribute) var_files (marvel.utils.config_tools.PipelineConfig attribute) var_id (marvel.extraction.extraction.ExtractionTask attribute) var_path (marvel.extraction.extraction.ExtractionTask attribute) var_sep (marvel.utils.config_tools.PipelineConfig attribute) Variant (class in marvel.extraction.core)

variant_output (marvel.utils.config_tools.PipelineConfig attribute) VariantExtraction (class in marvel.extraction.extraction) VariantExtractionStep (class in marvel.pipeline) VariantExtractor (class in marvel.extraction.extraction) VariantProcessor (class in marvel.extraction.core) VariantToGeneAggregator (class in marvel.extraction.aggregation) VcfReaderClass (class in marvel.extraction.extraction)