LUMA Methylation
Estimate LUMA methylation from normalized HpaII and MspI signals.
Description
LUMA normalizes enzyme signals to estimate a methylation proxy.
LUMA normalizes enzyme signals to estimate a methylation proxy.1
Estimate LUMA methylation from normalized HpaII and MspI signals.
When to use LUMA Methylation
Use this tool to estimate LUMA methylation from normalized HpaII and MspI signals.
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 LUMA 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 hpaiiSignal, mspiSignal, controlRatio using the field table and calculation rules, then run the tool.
- Read normalizedDigestionRatio, estimatedMethylationPercent. 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 |
|---|---|---|---|
| hpaiiSignal | HpaII signal | number; minimum: 0 | Required |
| mspiSignal | MspI signal | number; minimum: 0 | Required |
| controlRatio | Unmethylated control ratio | number; minimum: 0 | Required |
Enter nonnegative HpaII and positive MspI/control. Return ratio and estimate.
ratio=HpaII/MspI/control; methylation%=100(1−ratio) Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| normalizedDigestionRatio | Normalized digestion ratio | number; minimum: 0 |
| estimatedMethylationPercent | Estimated methylation (%) | number |
{
"input": {
"hpaiiSignal": 25,
"mspiSignal": 100,
"controlRatio": 0.5
},
"output": {
"normalizedDigestionRatio": 0.5,
"estimatedMethylationPercent": 50
}
}Limitations and assumptions
Estimates can be negative and are not clipped. No digestion efficiency or calibration is verified.
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 COBRA Retention: Calculate COBRA restriction cut-site retention from band intensities. For a complementary task, use Global Methylation Proxy: Apply a caller-supplied calibration to a LINE-1 global methylation proxy.
References
-
LUMA Methylation — tool.io
Similar or alternative tools
- COBRA Retention
Calculate COBRA restriction cut-site retention from band intensities.
- Global Methylation Proxy
Apply a caller-supplied calibration to a LINE-1 global methylation proxy.