Global Methylation Proxy
Apply a caller-supplied calibration to a LINE-1 global methylation proxy.
Description
LINE-1 can serve as a calibrated proxy rather than a direct genome-wide methylation measurement.
LINE-1 can serve as a calibrated proxy rather than a direct genome-wide methylation measurement.1
Apply a caller-supplied calibration to a LINE-1 global methylation proxy.
When to use Global Methylation Proxy
Use this tool to apply a caller-supplied calibration to a LINE-1 global methylation proxy.
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 Global Methylation Proxy 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 line1MethylationPercent, calibrationSlope, calibrationInterceptPercent using the field table and calculation rules, then run the tool.
- Read estimatedGlobalMethylationPercent, calibrationAdjustmentPoints. 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 |
|---|---|---|---|
| line1MethylationPercent | LINE-1 methylation (%) | number; minimum: 0; maximum: 100 | Required |
| calibrationSlope | Calibration slope | number | Required |
| calibrationInterceptPercent | Calibration intercept (%) | number | Required |
Enter LINE-1 0–100 and finite signed slope/intercept; return estimate and difference in percentage points.
estimate=slope×LINE1Percent+intercept Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| estimatedGlobalMethylationPercent | Estimated global methylation (%) | number |
| calibrationAdjustmentPoints | Calibration adjustment (percentage points) | number |
{
"input": {
"line1MethylationPercent": 70,
"calibrationSlope": 0.8,
"calibrationInterceptPercent": 10
},
"output": {
"estimatedGlobalMethylationPercent": 66,
"calibrationAdjustmentPoints": -4
}
}Limitations and assumptions
Estimate is not clipped to 0–100. No calibration fit or genome-wide measurement is performed.
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 Standard Interpolation: Linearly interpolate methylation percentage from two assay standards. For a complementary task, use LUMA Methylation: Estimate LUMA methylation from normalized HpaII and MspI signals.
References
-
Global Methylation Proxy — tool.io
Similar or alternative tools
- Methylation Standard Interpolation
Linearly interpolate methylation percentage from two assay standards.
- LUMA Methylation
Estimate LUMA methylation from normalized HpaII and MspI signals.