Description
Compare supplied nonclinical copy-number coordinates without inferring an allele or phenotype.
Pharmacogenomic records distinguish allele labels, copy counts, reference-sequence versions, coordinate systems, and evidence about chromosome phase. A balanced count or matching token can check a record without establishing the underlying genotype. Supplied activity values and interpretation rules remain separate from a current gene-specific clinical guideline.
Compare supplied nonclinical copy-number coordinates without inferring an allele or phenotype.
When to use this tool
Use Copy Number Reference Gap when you need this specific allele-token, reference-coordinate, copy-budget, or source-support check.
How to use the tool and how it works
- Enter suppliedCopyNumber, referenceCopyNumber. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read gap. Use the output convention below.
For nonnegative suppliedCopyNumber and referenceCopyNumber return gap=suppliedCopyNumber-referenceCopyNumber.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| suppliedCopyNumber | Nonnegative supplied copy-number estimate; fractional values permitted. | Required. Finite number; minimum 0. |
| referenceCopyNumber | Reference Copy Number | Required. Finite number; minimum 0. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| gap | Signed difference under the formula stated above. | Required. Finite number. |
{
"input": {
"suppliedCopyNumber": 3,
"referenceCopyNumber": 2
},
"output": {
"gap": 1
}
}Limitations and assumptions
- Fractional copy-number estimates are accepted. No assay normalization, uncertainty, gene-specific ploidy rule, structural-variant interpretation, or phenotype is calculated.
- Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.
- Numeric calculations use binary floating point unless exact decimal-integer arithmetic is explicitly stated. No hidden measurement tolerance or decimal rounding is added; nonfinite or out-of-contract results are rejected. Signed zero is exported as zero.
Alternative or Complementary methods
Use a current gene-specific nomenclature and a validated interpretation process when allele identity, phase, function, or clinical decisions matter. Verify source versions and reference coordinates before combining records.
References
Similar or alternative tools
- Pharmacogene Copy Number Token Field
Parse an explicit star-allele copy token; copies is zero when the copy number is unknown.
- Star Allele Copy Budget Remainder
Audit caller-supplied allele labels and copy counts without allele calling, phenotype inference or dosing guidance.