Clonal Distance Classifier
Classify methylation-derived clonal distance.
Description
Clonal-distance categories compare a supplied distance against chosen boundaries.
Clonal-distance categories compare a supplied distance against chosen boundaries.1
Classify methylation-derived clonal distance.
When to use Clonal Distance Classifier
Use this tool to classify methylation-derived clonal distance.
Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
How to use Clonal Distance Classifier and understand its results
- Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
- Enter methylationDistance, clonalThreshold, relatedThreshold using the field table and calculation rules, then run the tool.
- Read clonalMargin, relationship. The explanation below defines the units, signs, ordering and any flags or placeholder values.
- If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.
| Input field | Meaning | Value type; see rules below | Requirement |
|---|---|---|---|
| methylationDistance | Methylation distance | number; minimum: 0 | Required |
| clonalThreshold | Clonal threshold | number; minimum: 0 | Required |
| relatedThreshold | Related threshold | number; minimum: 0 | Required |
Enter nonnegative distance/ordered limits; return class and signed clonal margin.
≤clonal→clonal; ≤related→related; else distant Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| clonalMargin | Clonal threshold margin | number |
| relationship | Relationship | string; one of "clonal", "related", "distant" |
{
"input": {
"methylationDistance": 0.1,
"clonalThreshold": 0.2,
"relatedThreshold": 0.5
},
"output": {
"clonalMargin": 0.1,
"relationship": "clonal"
}
}Limitations and assumptions
No lineage or biological clonality is established.
Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use Methylation Haplotype Tally: Tally methylation haplotypes across phased binary reads. For a complementary task, use Epimutation Rate: Estimate epimutation rate per site and generation.
References
-
Clonal Distance Classifier — tool.io
Similar or alternative tools
- Methylation Haplotype Tally
Tally methylation haplotypes across phased binary reads.
- Epimutation Rate
Estimate epimutation rate per site and generation.