CPG Region Classifier

Classify a CpG’s distance from a caller-supplied island.

Description

CpG-region labels depend on distance from a supplied island and chosen shore/shelf bands.

CpG-region labels depend on distance from a supplied island and chosen shore/shelf bands.^[1]

Classify a CpG’s distance from a caller-supplied island.

When to use CPG Region Classifier

Use this tool to classify a CpG’s distance from a caller-supplied island.

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 CPG Region 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 cpgCoordinateBp, islandStartBp, islandEndBp, shoreDistanceBp, shelfDistanceBp using the field table and calculation rules, then run the tool.
Read distanceToIslandBp, regionClass. 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
cpgCoordinateBp	CpG coordinate bp	number	Required
islandStartBp	Island start bp	number	Required
islandEndBp	Island end bp	number	Required
shoreDistanceBp	Shore distance bp	number	Required
shelfDistanceBp	Shelf distance bp	number	Required

Enter finite position/ordered island bounds and nonnegative ordered distance widths. Return distance and inclusive category.

inside→island; distance≤shore→shore; ≤shelf→shelf; else open-sea

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

Output field	Meaning	Value type
distanceToIslandBp	Distance to island bp	number
regionClass	Region class	string; one of "island", "shore", "shelf", "open-sea"

json

{
  "input": {
    "cpgCoordinateBp": 2500,
    "islandStartBp": 1000,
    "islandEndBp": 2000,
    "shoreDistanceBp": 2000,
    "shelfDistanceBp": 4000
  },
  "output": {
    "distanceToIslandBp": 500,
    "regionClass": "shore"
  }
}

Limitations and assumptions

No CpG-density calling, genome build or chromosome 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 Context: Classify a cytosine as CG, CHG, or CHH context. For a complementary task, use meQTL Cis-Window: Check variant-CpG distance against a supplied cis window.

References

CPG Region Classifier — tool.io

Similar or alternative tools

Methylation Context
Classify a cytosine as CG, CHG, or CHH context.
meQTL Cis-Window
Check variant-CpG distance against a supplied cis window.