genetest package

Subpackages

• genetest.phenotypes package
  • Submodules
  • genetest.phenotypes.core module
  • genetest.phenotypes.text module
  • Module contents
• genetest.statistics package
  • Subpackages
    • genetest.statistics.models package
      • Submodules
      • genetest.statistics.models.linear module
      • genetest.statistics.models.logistic module
      • genetest.statistics.models.mixedlm module
      • genetest.statistics.models.survival module
      • Module contents
  • Submodules
  • genetest.statistics.core module
  • genetest.statistics.descriptive module
  • Module contents
• genetest.tests package
  • Submodules
  • 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
  • Module contents

Submodules

genetest.configuration module

class genetest.configuration.AnalysisConfiguration(filename)

Bases: object

Creates an instance of the class.

Parameters:filename (str) – The name of the configuration file.

configure_genotypes()

Configures the genotypes component.

configure_model()

Configures the statistics component.

configure_phenotypes()

Configures the phenotypes component.

get_genotypes()

Returns the genotypes container.

get_genotypes_args()

Returns the genotypes arguments.

get_genotypes_format()

Returns the genotypes format.

get_model_args()

Returns the statistics arguments.

get_model_formula()

Returns the model formula.

get_model_test()

Returns the statistics model.

get_phenotypes()

Returns the phenotypes container.

get_phenotypes_args()

Returns the phenotypes arguments.

get_phenotypes_format()

Returns the phenotypes format.

static retrieve_arguments(config)

Retrieves arguments from the configuration.

Parameters:config (configparser.SectionProxy) – The section’s configuration. Returns:The arguments extracted from this section’s configuration. Return type:dict

static retrieve_options(config)

Retrieves options from the configuration.

Parameters:config (configparser.SectionProxy) – The section’s configuration. Returns:The optional arguments. Return type:dict

Note

Only the restricted ‘options’ key is parsed, and has the following format: keyword=type:value (e.g. sep=str:,). If there are multiple keyword/values, they are separated by a single coma.

genetest.version module

Module contents

genetest.test(verbosity=1)

Execute all the tests.