ExpressionInputConfig

class VmaxBuilder.config.dataclasses.ExpressionInputConfig(id_type: str | None = 'ensembl', level: str = 'gene', sample_type_map: dict[str, str] | str | None = None, transformation_state: str = 'log', data_type: str = 'TPM', thresholding: bool | str = False, transcript_aggregation_policy: str = 'sum', id_translation_provider: str = 'auto', id_translation_species: str | None = None, id_translation_max_workers: int = 8, id_translation_batch_size: int = 500)[source]

Generated: validation needed.

Description:

Expression input option group used by protein-stage expression->protein flow.

Parameters:

  • id_type (str | None) – Identifier provider for expression features.

  • level (str) – Gene or transcript level granularity.

  • sample_type_map (dict[str, str] | str | None) – Mapping from expression sample columns to PTR tissue/sample columns used by expression+PTR protein flow. str maps all expression columns to one PTR column; dict maps each expression column individually.

  • transformation_state (str) – Data transform state, e.g. log or linear.

  • data_type (str) – Expression quantification type, e.g. TPM, geTMM, raw_reads.

  • thresholding (bool | str) – Disabled flag or thresholding strategy name.

  • transcript_aggregation_policy (str) – Transcript-to-gene aggregation policy.

  • id_translation_provider (str) – Identifier translation provider key.

  • id_translation_species (str | None) – Optional species hint for API lookups.

  • id_translation_max_workers (int) – Maximum worker threads for translation API calls.

  • id_translation_batch_size (int) – Identifier batch size for translation API calls.

Public Methods

id_type

level

sample_type_map

transformation_state

data_type

thresholding

transcript_aggregation_policy

id_translation_provider

id_translation_species

id_translation_max_workers

id_translation_batch_size