Builds a comprehensive HTML report for Module 1 run parameters, input gates, motif-supported canonical support, prediction output integrity, correlation diagnostics, condition-level CraftGRN multiomic input QC, metadata-aware PCA, footprint alignment summaries, warning checks, and interactive Binding, Co-binding, and Motif review. The report can consume a `predict_tfbs()` result, a step-by-step Module 1 result list, or a Module 1 output directory.
Usage
build_module1_qc_report(
module1,
omics_data = NULL,
output_dir = NULL,
report_name = "module1_qc_report.html",
scan_predicted_tfbs = TRUE,
top_n = 20L,
project_config = NULL,
project_date = NULL,
build_tfbs_explorer = TRUE,
default_condition = NULL,
recompute_correlation_hist = FALSE,
correlation_hist_cores = NULL,
verbose = TRUE
)Arguments
- module1
Module 1 result list or Module 1 output directory.
- omics_data
Optional CraftGRN multiomic object. Used when `module1` is an output directory or does not contain `omics_data`.
- output_dir
Directory where the HTML report should be written. If `NULL`, the report is written under `reports` inside the Module 1 output directory when available.
- report_name
HTML report filename.
- scan_predicted_tfbs
Logical; if `TRUE`, scan predicted TFBS chunks to summarize top TFs and condition support. This is comprehensive but can take extra time on full projects.
- top_n
Number of TFs to show in top-TF summaries.
- project_config
Optional YAML path or list used for parameter provenance in the Run Summary.
- project_date
Optional project date displayed in the report title.
- build_tfbs_explorer
Logical; embed the interactive Binding, Co-binding, and Motif explorer sections in the QC report.
- default_condition
Optional initial condition for TFBS report previews and the linked explorer.
- recompute_correlation_hist
Logical; recompute the all-evaluated correlation histogram for a legacy run that predates the compact histogram artifact. This requires the matching multiomic object and exact saved canonical-bound footprint set.
- correlation_hist_cores
Optional worker count for legacy histogram recomputation.
- verbose
Emit concise progress messages.