DMR Window Merger

Merge adjacent DMR windows within a selected distance.

Description

Candidate DMR windows can be merged by proximity separately from testing methylation differences.

Candidate DMR windows can be merged by proximity separately from testing methylation differences.^[1]

Merge adjacent DMR windows within a selected distance.

When to use DMR Window Merger

Use this tool to merge adjacent DMR windows within a selected 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 DMR Window Merger 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 startsBp, endsBp, maximumGapBp using the field table and calculation rules, then run the tool.
Read mergedStartsBp, mergedEndsBp, regionCount. 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
startsBp	Starts bp	list of number	Required
endsBp	Ends bp	list of number	Required
maximumGapBp	Maximum gap bp	number	Required

Enter nonempty aligned start-sorted intervals with start≤end and nonnegative gap. Merge overlaps/touching/qualifying gaps; return starts, ends and count.

merge when nextStart−currentEnd≤maximumGap

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
mergedStartsBp	Merged starts bp	list of number
mergedEndsBp	Merged ends bp	list of number
regionCount	Region count	number

json

{
  "input": {
    "startsBp": [
      10,
      25,
      100
    ],
    "endsBp": [
      20,
      30,
      110
    ],
    "maximumGapBp": 10
  },
  "output": {
    "mergedStartsBp": [
      10,
      100
    ],
    "mergedEndsBp": [
      30,
      110
    ],
    "regionCount": 2
  }
}

Limitations and assumptions

No chromosome separation or methylation testing is applied. Signed/fractional coordinates are accepted.

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 Super-Enhancer Stitching: Stitch enhancer intervals separated by a supplied maximum distance. For a complementary task, use DMP Significance Gate: Gate single-CpG differential methylation by FDR and effect size.

References

DMR Window Merger — tool.io

Similar or alternative tools

Super-Enhancer Stitching
Stitch enhancer intervals separated by a supplied maximum distance.
DMP Significance Gate
Gate single-CpG differential methylation by FDR and effect size.