Index

A

AnalysisConfiguration (class in genetest.configuration)

C

close() (genetest.phenotypes.core.PhenotypesContainer method) (genetest.phenotypes.text.TextPhenotypes method)

configure_genotypes() (genetest.configuration.AnalysisConfiguration method) configure_model() (genetest.configuration.AnalysisConfiguration method) configure_phenotypes() (genetest.configuration.AnalysisConfiguration method)

F

fit() (genetest.statistics.core.StatsModels method) (genetest.statistics.models.linear.StatsLinear method) (genetest.statistics.models.logistic.StatsLogistic method) (genetest.statistics.models.mixedlm.StatsMixedLM method) (genetest.statistics.models.survival.StatsCoxPH method)

G

genetest (module) genetest.configuration (module) genetest.phenotypes (module) genetest.phenotypes.core (module) genetest.phenotypes.text (module) genetest.statistics (module) genetest.statistics.core (module) genetest.statistics.descriptive (module) genetest.statistics.models (module) genetest.statistics.models.linear (module) genetest.statistics.models.logistic (module) genetest.statistics.models.mixedlm (module) genetest.statistics.models.survival (module) genetest.tests (module) genetest.tests.test_configuration (module) genetest.tests.test_coxph (module) genetest.tests.test_descriptive_stats (module) genetest.tests.test_linear (module) genetest.tests.test_logistic (module) genetest.tests.test_mixedlm (module)

genetest.tests.test_phenotypes (module) genetest.tests.test_stats_core (module) genetest.version (module) get_genotypes() (genetest.configuration.AnalysisConfiguration method) get_genotypes_args() (genetest.configuration.AnalysisConfiguration method) get_genotypes_format() (genetest.configuration.AnalysisConfiguration method) get_maf() (in module genetest.statistics.descriptive) get_model_args() (genetest.configuration.AnalysisConfiguration method) get_model_formula() (genetest.configuration.AnalysisConfiguration method) get_model_test() (genetest.configuration.AnalysisConfiguration method) get_nb_samples() (genetest.phenotypes.core.PhenotypesContainer method) (genetest.phenotypes.text.TextPhenotypes method) get_nb_variables() (genetest.phenotypes.core.PhenotypesContainer method) (genetest.phenotypes.text.TextPhenotypes method) get_phenotypes() (genetest.configuration.AnalysisConfiguration method) (genetest.phenotypes.core.PhenotypesContainer method) (genetest.phenotypes.text.TextPhenotypes method) get_phenotypes_args() (genetest.configuration.AnalysisConfiguration method) get_phenotypes_format() (genetest.configuration.AnalysisConfiguration method) get_sex() (genetest.phenotypes.core.PhenotypesContainer method)

I

is_repeated() (genetest.phenotypes.core.PhenotypesContainer method) (genetest.phenotypes.text.TextPhenotypes method)

K

keep_samples() (genetest.phenotypes.core.PhenotypesContainer method) (genetest.phenotypes.text.TextPhenotypes method)

M

merge() (genetest.phenotypes.text.TextPhenotypes method)

P

parse_modelspec() (in module genetest.statistics.core)

PhenotypesContainer (class in genetest.phenotypes.core)

R

retrieve_arguments() (genetest.configuration.AnalysisConfiguration static method)

retrieve_options() (genetest.configuration.AnalysisConfiguration static method)

S

setUp() (genetest.tests.test_coxph.TestStatsCoxPH method) (genetest.tests.test_linear.TestStatsLinear method) (genetest.tests.test_logistic.TestStatsLogistic method) (genetest.tests.test_mixedlm.TestStatsMixedLM method) (genetest.tests.test_phenotypes.TestText method) (genetest.tests.test_stats_core.TestStatsLinear method) setUpClass() (genetest.tests.test_configuration.TestAnalysisConfiguration class method) (genetest.tests.test_coxph.TestStatsCoxPH class method) (genetest.tests.test_linear.TestStatsLinear class method) (genetest.tests.test_logistic.TestStatsLogistic class method) (genetest.tests.test_mixedlm.TestStatsMixedLM class method)

StatsCoxPH (class in genetest.statistics.models.survival) StatsError StatsLinear (class in genetest.statistics.models.linear) StatsLogistic (class in genetest.statistics.models.logistic) StatsMixedLM (class in genetest.statistics.models.mixedlm) StatsModels (class in genetest.statistics.core)

T

tearDown() (genetest.tests.test_phenotypes.TestText method) tearDownClass() (genetest.tests.test_configuration.TestAnalysisConfiguration class method) (genetest.tests.test_coxph.TestStatsCoxPH class method) (genetest.tests.test_linear.TestStatsLinear class method) (genetest.tests.test_logistic.TestStatsLogistic class method) (genetest.tests.test_mixedlm.TestStatsMixedLM class method) test() (in module genetest) test__create_model() (genetest.tests.test_stats_core.TestStatsLinear method) test__create_model_no_intercept() (genetest.tests.test_stats_core.TestStatsLinear method) test__create_model_with_interaction() (genetest.tests.test_stats_core.TestStatsLinear method) test__create_model_with_interaction2() (genetest.tests.test_stats_core.TestStatsLinear method) test__create_model_with_interaction_not_in_predictors() (genetest.tests.test_stats_core.TestStatsLinear method) test_bad_subset_phenotypes() (genetest.tests.test_phenotypes.TestText method) test_close() (genetest.tests.test_phenotypes.TestCore method) test_coxph_gwas() (genetest.tests.test_coxph.TestStatsCoxPH method) test_coxph_gwas_inter() (genetest.tests.test_coxph.TestStatsCoxPH method) test_coxph_snp1() (genetest.tests.test_coxph.TestStatsCoxPH method) test_coxph_snp1_inter() (genetest.tests.test_coxph.TestStatsCoxPH method) test_coxph_snp1_inter_categorical() (genetest.tests.test_coxph.TestStatsCoxPH method) test_coxph_snp2() (genetest.tests.test_coxph.TestStatsCoxPH method) test_coxph_snp2_inter() (genetest.tests.test_coxph.TestStatsCoxPH method) test_coxph_snp3() (genetest.tests.test_coxph.TestStatsCoxPH method) test_coxph_snp3_inter() (genetest.tests.test_coxph.TestStatsCoxPH method) test_coxph_snp4() (genetest.tests.test_coxph.TestStatsCoxPH method) test_coxph_snp4_inter() (genetest.tests.test_coxph.TestStatsCoxPH method) test_duplicated_sex() (genetest.tests.test_phenotypes.TestText method) test_extra_section() (genetest.tests.test_configuration.TestAnalysisConfiguration method) test_get_maf_flip() (genetest.tests.test_descriptive_stats.TestDescriptiveStats method) test_get_maf_flip_sex() (genetest.tests.test_descriptive_stats.TestDescriptiveStats method) test_get_maf_no_valid_genotypes() (genetest.tests.test_descriptive_stats.TestDescriptiveStats method) test_get_maf_no_valid_genotypes_sex() (genetest.tests.test_descriptive_stats.TestDescriptiveStats method) test_get_maf_with_null() (genetest.tests.test_descriptive_stats.TestDescriptiveStats method) test_get_maf_with_null_sex() (genetest.tests.test_descriptive_stats.TestDescriptiveStats method) test_get_maf_without_null() (genetest.tests.test_descriptive_stats.TestDescriptiveStats method) test_get_maf_without_null_sexes() (genetest.tests.test_descriptive_stats.TestDescriptiveStats method) test_get_phenotypes() (genetest.tests.test_phenotypes.TestCore method) test_get_sex() (genetest.tests.test_phenotypes.TestText method) test_get_sex_no_attribute() (genetest.tests.test_phenotypes.TestCore method) test_invalid_genotype_format() (genetest.tests.test_configuration.TestAnalysisConfiguration method) test_invalid_phenotype_format() (genetest.tests.test_configuration.TestAnalysisConfiguration method) test_invalid_sex() (genetest.tests.test_phenotypes.TestText method) test_invalid_test() (genetest.tests.test_configuration.TestAnalysisConfiguration method) test_linear_gwas() (genetest.tests.test_linear.TestStatsLinear method) test_linear_gwas_inter() (genetest.tests.test_linear.TestStatsLinear method) test_linear_snp1() (genetest.tests.test_linear.TestStatsLinear method) test_linear_snp1_inter() (genetest.tests.test_linear.TestStatsLinear method) test_linear_snp1_inter_categorical() (genetest.tests.test_linear.TestStatsLinear method) test_linear_snp2() (genetest.tests.test_linear.TestStatsLinear method) test_linear_snp2_inter() (genetest.tests.test_linear.TestStatsLinear method) test_linear_snp3() (genetest.tests.test_linear.TestStatsLinear method) test_linear_snp3_inter() (genetest.tests.test_linear.TestStatsLinear method) test_linear_snp4() (genetest.tests.test_linear.TestStatsLinear method)

test_linear_snp4_inter() (genetest.tests.test_linear.TestStatsLinear method) test_linear_snp5() (genetest.tests.test_linear.TestStatsLinear method) test_linear_snp5_inter() (genetest.tests.test_linear.TestStatsLinear method) test_logistic_gwas() (genetest.tests.test_logistic.TestStatsLogistic method) test_logistic_gwas_inter() (genetest.tests.test_logistic.TestStatsLogistic method) test_logistic_snp1() (genetest.tests.test_logistic.TestStatsLogistic method) test_logistic_snp1_inter() (genetest.tests.test_logistic.TestStatsLogistic method) test_logistic_snp1_inter_categorical() (genetest.tests.test_logistic.TestStatsLogistic method) test_logistic_snp2() (genetest.tests.test_logistic.TestStatsLogistic method) test_logistic_snp2_inter() (genetest.tests.test_logistic.TestStatsLogistic method) test_logistic_snp3() (genetest.tests.test_logistic.TestStatsLogistic method) test_logistic_snp3_inter() (genetest.tests.test_logistic.TestStatsLogistic method) test_missing_genotype_format() (genetest.tests.test_configuration.TestAnalysisConfiguration method) test_missing_phenotype_format() (genetest.tests.test_configuration.TestAnalysisConfiguration method) test_missing_section() (genetest.tests.test_configuration.TestAnalysisConfiguration method) test_missing_test() (genetest.tests.test_configuration.TestAnalysisConfiguration method) test_mixedlm_gwas() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_gwas_inter() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp1_inter_ml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp1_inter_reml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp1_ml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp1_reml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp2_inter_ml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp2_inter_reml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp2_ml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp2_reml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp3_inter_ml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp3_inter_reml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp3_ml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp3_reml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp4_inter_ml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp4_inter_reml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp4_ml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_mixedlm_snp4_reml() (genetest.tests.test_mixedlm.TestStatsMixedLM method) test_multiple_missing_values() (genetest.tests.test_phenotypes.TestText method) test_normal_functionality() (genetest.tests.test_configuration.TestAnalysisConfiguration method) (genetest.tests.test_phenotypes.TestText method) test_one_other_missing_value() (genetest.tests.test_phenotypes.TestText method) test_repeated_measurements() (genetest.tests.test_phenotypes.TestText method) test_specific_column_missing_value() (genetest.tests.test_phenotypes.TestText method) test_string_representation() (genetest.tests.test_phenotypes.TestText method) test_subset_phenotypes() (genetest.tests.test_phenotypes.TestText method) test_undefined_sex_column() (genetest.tests.test_phenotypes.TestText method) TestAnalysisConfiguration (class in genetest.tests.test_configuration) TestCore (class in genetest.tests.test_phenotypes) TestDescriptiveStats (class in genetest.tests.test_descriptive_stats) TestStatsCoxPH (class in genetest.tests.test_coxph) TestStatsLinear (class in genetest.tests.test_linear) (class in genetest.tests.test_stats_core) TestStatsLogistic (class in genetest.tests.test_logistic) TestStatsMixedLM (class in genetest.tests.test_mixedlm) TestText (class in genetest.tests.test_phenotypes) TextPhenotypes (class in genetest.phenotypes.text)