Delta Beta Effect Classifier

Classify differential methylation effect using caller-supplied beta thresholds.

Description

Delta beta expresses signed methylation-fraction change; magnitude bands use selected cutoffs.

Delta beta expresses signed methylation-fraction change; magnitude bands use selected cutoffs.^[1]

Classify differential methylation effect using caller-supplied beta thresholds.

When to use Delta Beta Effect Classifier

Use this tool to classify differential methylation effect using caller-supplied beta thresholds.

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 Delta Beta Effect 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 controlBeta, treatmentBeta, smallEffectAt, largeEffectAt using the field table and calculation rules, then run the tool.
Read deltaBeta, absoluteEffect, effectBand. 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
controlBeta	Control beta	number	Required
treatmentBeta	Treatment beta	number	Required
smallEffectAt	Small effect at	number	Required
largeEffectAt	Large effect at	number	Required

Enter beta values 0–1 and nonnegative ordered cutoffs; return delta/classification.

delta=treatment−control; large if abs(delta)≥large, moderate if ≥small, else small

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

Output field	Meaning	Value type
deltaBeta	Delta beta	number
absoluteEffect	Absolute effect	number
effectBand	Effect band	string; one of "small", "moderate", "large"

json

{
  "input": {
    "controlBeta": 0.2,
    "treatmentBeta": 0.5,
    "smallEffectAt": 0.05,
    "largeEffectAt": 0.2
  },
  "output": {
    "deltaBeta": 0.3,
    "absoluteEffect": 0.3,
    "effectBand": "large"
  }
}

Limitations and assumptions

Cutoffs may exceed one. No significance or causal interpretation is supplied.

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 DMP Significance Gate: Gate single-CpG differential methylation by FDR and effect size. For a complementary task, use Methylation M Value: Convert a methylation beta fraction into a base-two logit M-value.

References

Delta Beta Effect Classifier — tool.io

Similar or alternative tools

DMP Significance Gate
Gate single-CpG differential methylation by FDR and effect size.
Methylation M Value
Convert a methylation beta fraction into a base-two logit M-value.