Single-CpG Methylation

Calculate single-CpG methylation after background correction.

Description

Single-CpG methylation is the methylated share of usable channel signal.

Single-CpG methylation is the methylated share of usable channel signal.^[1]

Calculate single-CpG methylation after background correction.

When to use Single-CpG Methylation

Use this tool to calculate single-CpG methylation after background correction.

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 Single-CpG Methylation 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 methylatedSignal, unmethylatedSignal, backgroundSignal using the field table and calculation rules, then run the tool.
Read correctedMethylatedSignal, correctedUnmethylatedSignal, methylationPercent. 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
methylatedSignal	Methylated signal	number; minimum: 0	Required
unmethylatedSignal	Unmethylated signal	number; minimum: 0	Required
backgroundSignal	Background signal	number; minimum: 0	Required

Enter nonnegative signals/background and require positive corrected total. Return corrected signals and percentage.

M=max(0,methylated−background); U=max(0,unmethylated−background); percent=100M/(M+U)

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

Output field	Meaning	Value type
correctedMethylatedSignal	Corrected methylated signal	number; minimum: 0
correctedUnmethylatedSignal	Corrected unmethylated signal	number; minimum: 0
methylationPercent	Single-CpG methylation (%)	number; minimum: 0; maximum: 100

json

{
  "input": {
    "methylatedSignal": 80,
    "unmethylatedSignal": 30,
    "backgroundSignal": 5
  },
  "output": {
    "correctedMethylatedSignal": 75,
    "correctedUnmethylatedSignal": 25,
    "methylationPercent": 75
  }
}

Limitations and assumptions

No conversion efficiency, probe bias or confidence interval is modeled.

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 M Value: Convert a methylation beta fraction into a base-two logit M-value. For a complementary task, use Methylation Beta From M: Invert a base-two methylation M-value into a beta fraction.

References

Single-CpG Methylation — tool.io

Similar or alternative tools

Methylation M Value
Convert a methylation beta fraction into a base-two logit M-value.
Methylation Beta From M
Invert a base-two methylation M-value into a beta fraction.