Prepare condition-native Module 3 links — module3_prepare_condition

Builds per-condition TF-peak-gene links from Module 2 final links and the CraftGRN multiomic condition matrices. This path is used for condition topic models that should not depend on differential-link comparisons.

Usage

module3_prepare_condition_links(
  module2,
  multiomic_data,
  conditions = NULL,
  output_dir,
  threshold_fp_score = 0,
  threshold_gene_expr = 0,
  threshold_tf_expr = -Inf,
  output_format = c("auto", "parquet", "csv"),
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

module2: Module 2 output object or output directory.
multiomic_data: CraftGRN multiomic object.
conditions: Optional condition IDs to keep.
output_dir: Directory for per-condition link files and manifest.
threshold_fp_score: Minimum condition footprint score.
threshold_gene_expr: Minimum target-gene expression.
threshold_tf_expr: Minimum TF expression.
output_format: Output format: auto, parquet, or csv.
overwrite: Overwrite existing condition-link files.
verbose: Emit concise progress messages.

Value

A list containing the manifest and summary tables.