Heterochromatin Spread
Measure heterochromatin spread relative to a reference.
Description
Boundary displacement summarizes supplied heterochromatin-spread measurements.
Boundary displacement summarizes supplied heterochromatin-spread measurements.1
Measure heterochromatin spread relative to a reference.
When to use Heterochromatin Spread
Use this tool to measure heterochromatin spread relative to a reference.
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 Heterochromatin Spread 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 sourceBoundaryBp, observedBoundaryBp, referenceBoundaryBp using the field table and calculation rules, then run the tool.
- Read spreadExtentBp, spreadChangeBp, direction. 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 |
|---|---|---|---|
| sourceBoundaryBp | Source boundary | number | Required |
| observedBoundaryBp | Observed boundary | number | Required |
| referenceBoundaryBp | Reference boundary | number | Required |
Enter finite signed positions. Return extent/change and expanded, contracted or unchanged by change sign.
extent=observed−source; change=observed−reference Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| spreadExtentBp | Spread extent | number |
| spreadChangeBp | Spread change | number |
| direction | Direction | string; one of "expanded", "contracted", "unchanged" |
{
"input": {
"sourceBoundaryBp": 100,
"observedBoundaryBp": 500,
"referenceBoundaryBp": 400
},
"output": {
"spreadExtentBp": 400,
"spreadChangeBp": 100,
"direction": "expanded"
}
}Limitations and assumptions
No chromosome, traversal direction or boundary detection is inferred.
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 TAD Boundary Distance: Measure adjacent TAD boundary distances. For a complementary task, use Insulation Local Minimum: Find the lowest insulation score within an interior search range.
References
-
Heterochromatin Spread — tool.io
Similar or alternative tools
- TAD Boundary Distance
Measure adjacent TAD boundary distances.
- Insulation Local Minimum
Find the lowest insulation score within an interior search range.