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CLI contract

Rscript cancerppir.R input.csv results_dir string_cache [score_threshold] [top_n] [run_enrichment] [--case-id ID]
Rscript cancerppir.R --help
Rscript cancerppir.R --version
Position Argument Requirement
1 input.csv Existing delimited input table
2 results_dir Root output directory
3 string_cache Local STRING cache directory
4 score_threshold Optional integer from 1 to 1000; default 400
5 top_n Optional positive integer; default 30
6 run_enrichment Optional TRUE or FALSE; default TRUE

Named option: --case-id ID sets a pseudonymous identifier containing 1-64 safe ASCII characters. --case-id=ID is also accepted.

Input preflight

The first positional argument must satisfy the scientific input contract. Column identity is determined from explicit recognized headers; positional fallback is not available. Raw pvalue, base-2 tumor-versus-reference logFC, complete finite numeric values and unique gene symbols are required. Input-contract failures return a non-zero exit status before STRING initialization.

Exactly three to six positional arguments are accepted. Additional arguments are rejected rather than ignored. Invalid integers, fractional values, out-of-range thresholds, and unrecognized Boolean values produce a non-zero exit status before network analysis begins.

The case_id must start with a letter or digit and may contain only ASCII letters, digits, ., _ and -; it must not end in . or use a reserved Windows device name. It determines the case-folder name and is the recommended privacy-safe interface for patient data. If it is omitted, CancerPPIr retains the legacy input-basename behavior and prints a reminder.

The case folder must not already exist. CancerPPIr never overwrites or reuses a result folder. Outputs are generated in a sibling staging directory and atomically published only after all output and provenance checks pass. Progress messages show the current stage and elapsed run time.

For an intentional rerun, choose a new pseudonymous ID such as DEMO01_run2 or move the previous case folder first. CancerPPIr deliberately has no implicit overwrite mode.

Rscript cancerppir.R --help is the executable source of truth; --version prints the program version and exits without starting an analysis.