Allele–Methylation Coupling

Detect allele-specific methylation from phased read counts.

Description

Allelic methylation contrast compares two supplied methylated read shares.

Allelic methylation contrast compares two supplied methylated read shares.^[1]

Detect allele-specific methylation from phased read counts.

When to use Allele–Methylation Coupling

Use this tool to detect allele-specific methylation from phased read counts.

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 Allele–Methylation Coupling 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 alleleOneMethylated, alleleOneTotal, alleleTwoMethylated, alleleTwoTotal, minimumDifferencePoints using the field table and calculation rules, then run the tool.
Read absoluteDifferencePoints, coupled. 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
alleleOneMethylated	Allele-one methylated reads	integer; minimum: 0	Required
alleleOneTotal	Allele-one total reads	integer; minimum: 1	Required
alleleTwoMethylated	Allele-two methylated reads	integer; minimum: 0	Required
alleleTwoTotal	Allele-two total reads	integer; minimum: 1	Required
minimumDifferencePoints	Minimum difference	number; minimum: 0	Required

Enter positive integer totals, integer methylated counts within totals and nonnegative minimum; compute each allele percentage internally and return the absolute percentage-point difference and inclusive flag.

differencePoints=abs(100methA/totalA−100methB/totalB)

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

Output field	Meaning	Value type
absoluteDifferencePoints	Absolute methylation difference	number; minimum: 0
coupled	Allele-specific coupling detected	boolean

json

{
  "input": {
    "alleleOneMethylated": 80,
    "alleleOneTotal": 100,
    "alleleTwoMethylated": 20,
    "alleleTwoTotal": 100,
    "minimumDifferencePoints": 40
  },
  "output": {
    "absoluteDifferencePoints": 60,
    "coupled": true
  }
}

Limitations and assumptions

No phasing, statistical association or biological coupling mechanism is evaluated.

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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use XCI Escapee Discordance: Flag XCI escapee candidates with expression skew but balanced methylation. For a complementary task, use Imprinting Loss: Flag loss of imprinting from biallelic expression.

References

Allele–Methylation Coupling — tool.io

Similar or alternative tools

XCI Escapee Discordance
Flag XCI escapee candidates with expression skew but balanced methylation.
Imprinting Loss
Flag loss of imprinting from biallelic expression.