PTRInputConfig

class VmaxBuilder.config.dataclasses.PTRInputConfig(id_type: str = 'ensembl', level: str = 'gene', pretransformed_type: str = 'linear', partial_missing_use_weighted: bool = True, partial_missing_weighted_statistic: str = 'median', partial_missing_imputation_statistic: str = 'median', unobserved_gene_imputation_strategy: str = 'sample_after_imputation', unobserved_gene_imputation_statistic: str = 'median', use_special_groups_for_unobserved_imputation: bool = False, special_gene_groups: dict[str, list[str]] | None = None, impute_from_metabolic_genes_only: bool = True)

Generated: validation needed.

Description:

PTR input option group used by expression+PTR protein abundance flow.

Parameters:

• id_type (str) – Identifier provider for PTR features.

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

• pretransformed_type (str) – Log-scale used in raw PTR input before linear conversion. One of linear, log10, log2, ln.

• partial_missing_use_weighted (bool) – Whether within-sample imputation should apply per-sample weighting. True keeps weighted column scaling; False uses unweighted row-statistic imputation.

• partial_missing_weighted_statistic (str) – Column statistic used for weighted scaling during within-sample imputation. One of median, mean, mode, max, min.

• partial_missing_imputation_statistic (str) – Row statistic used for within-sample imputation of observed-but-missing PTR values. One of median, mean, mode, max, min.

• unobserved_gene_imputation_strategy (str) – Strategy used to fill genes present in expression but absent from PTR. One of sample_after_imputation, sample_before_imputation.

• unobserved_gene_imputation_statistic (str) – Per-sample statistic used when imputing unobserved genes. One of median, mean, max, min.

• use_special_groups_for_unobserved_imputation (bool) – Whether to impute configured special gene groups independently.

• special_gene_groups (dict[str, list[str]] | None) – Optional custom grouping entries to impute independently. Values may contain gene IDs or reaction IDs; transport_reactions may be given with an empty list to auto-resolve transport-associated genes from model.

• impute_from_metabolic_genes_only (bool) – Restrict PTR prior to imputation to genes found in the metabolic model.

Public Methods

id_type
level
pretransformed_type
partial_missing_use_weighted
partial_missing_weighted_statistic
partial_missing_imputation_statistic
unobserved_gene_imputation_strategy
unobserved_gene_imputation_statistic
use_special_groups_for_unobserved_imputation
special_gene_groups
impute_from_metabolic_genes_only