Predict TF targets through TFBS-target and TF-target correlations
Source:R/utils_step2_predict_tf_targets.R
predict_tf_targets.RdPredict TF targets through TFBS-target and TF-target correlations
Usage
predict_tf_targets(
multiomic_data,
predicted_tfbs,
gene_tss = NULL,
regulatory_prior = NULL,
project_config = NULL,
output_dir = NULL,
max_distance_bp = NULL,
n_cores = NULL,
output_format = c("auto", "parquet", "csv"),
verbose = TRUE,
write_qc_report = TRUE,
qc_report_validate = FALSE
)Arguments
- multiomic_data
CraftGRN multiomic object returned by `load_prep_multiomic_data()`.
- predicted_tfbs
Compact Module 1 predicted TFBS table or manifest path.
- gene_tss
Optional gene TSS annotation table or path. If `NULL`, the table is resolved from `project_config$gene_tss` or generated from the configured `ref_genome`.
- regulatory_prior
Optional generic FP-target regulatory prior.
- project_config
Optional project YAML path or list.
- output_dir
Optional output directory.
- max_distance_bp
Maximum signed distance to TSS for window candidates.
- n_cores
Number of CPU cores.
- output_format
Output format: auto, parquet, or csv.
- verbose
Emit concise progress messages.
- write_qc_report
Write a Module 2 HTML QC report when `output_dir` is supplied.
- qc_report_validate
Run relational integrity checks in the automatic QC report.