TAD Boundary Distance
Measure adjacent TAD boundary distances.
Description
TAD boundary spacing summarizes positions already assigned as boundaries.
TAD boundary spacing summarizes positions already assigned as boundaries.1
Measure adjacent TAD boundary distances.
When to use TAD Boundary Distance
Use this tool to measure adjacent TAD boundary distances.
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 TAD Boundary Distance 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 tadBoundaryPositionsBp using the field table and calculation rules, then run the tool.
- Read adjacentDistancesBp, meanDistanceBp, minimumDistanceBp. 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 |
|---|---|---|---|
| tadBoundaryPositionsBp | TAD boundary positions (bp) | list of number | Required |
Enter at least two strictly increasing finite positions; return adjacent gaps, mean and minimum.
gap[i]=boundary[i+1]−boundary[i] Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| adjacentDistancesBp | Adjacent boundary distances (bp) | list of number |
| meanDistanceBp | Mean TAD boundary distance (bp) | number; minimum: 0 |
| minimumDistanceBp | Minimum boundary distance (bp) | number; minimum: 0 |
{
"input": {
"tadBoundaryPositionsBp": [
0,
100,
300
]
},
"output": {
"adjacentDistancesBp": [
100,
200
],
"meanDistanceBp": 150,
"minimumDistanceBp": 100
}
}Limitations and assumptions
Signed/fractional coordinates are accepted. No chromosome or domain detection is performed.
Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use Insulation Local Minimum: Find the lowest insulation score within an interior search range. For a complementary task, use DMR Window Merger: Merge adjacent DMR windows within a selected distance.
References
-
TAD Boundary Distance — tool.io
Similar or alternative tools
- Insulation Local Minimum
Find the lowest insulation score within an interior search range.
- DMR Window Merger
Merge adjacent DMR windows within a selected distance.