Prepare differential links for Module 3
Source:R/utils_step3_compact_diff_links.R
module3_prepare_differential_links.RdConverts Module 2 link manifests into the filtered differential-link files consumed by CraftGRN topic-modeling utilities. This avoids writing full per-condition GRN matrices and keeps Module 3 compatible with the existing `*_filtered_links_up.csv` and `*_filtered_links_down.csv` contract.
Usage
module3_prepare_differential_links(
module2,
multiomic_data,
compar = NULL,
project_config = NULL,
output_dir = NULL,
n_cores = NULL,
pseudocount = 1,
rna_de_results = NULL,
fp_signal_mode = NULL,
overwrite = FALSE,
verbose = TRUE
)Arguments
- module2
Module 2 object returned by [predict_tf_targets()] or a path to a Module 2 output directory containing `module2_manifest.csv`.
- multiomic_data
CraftGRN multiomic object returned by [load_prep_multiomic_data()].
- compar
Comparison table or CSV path with `cond1_label` and `cond2_label`. If `NULL`, `data/episcope_comparisons.csv` under `base_dir` is used.
- project_config
Project config list or YAML path.
- output_dir
Directory for filtered differential links. If `NULL`, `regulatory_topics/differential_links` under `base_dir` is used.
- n_cores
Number of data.table threads to use while reading and joining chunks. Defaults to all available cores. Comparison-level parallelism is controlled by `module3_comparison_workers` in the project config and defaults to 1 for RAM safety.
- pseudocount
Pseudocount for log2 fold-change calculations.
- rna_de_results
Optional standardized RNA differential expression table or CSV. When provided, target-gene and TF log2 fold changes are read from this table and direct condition fold changes are used only for missing genes.
- fp_signal_mode
FP signal used for differential FP fold changes. actual uses the measured FP score in both conditions. link_padded sets the FP score to zero in conditions where the TF-FP-gene link is not active before calculating delta_fp_score and log2FC_fp_score.
- overwrite
Overwrite existing filtered link files.
- verbose
Emit concise progress messages.