DMP Significance Gate
Gate single-CpG differential methylation by FDR and effect size.
Description
A differential-methylation gate combines supplied statistical and effect criteria.
A differential-methylation gate combines supplied statistical and effect criteria.1
Gate single-CpG differential methylation by FDR and effect size.
When to use DMP Significance Gate
Use this tool to gate single-CpG differential methylation by FDR and effect size.
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 DMP Significance Gate 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 adjustedP, maximumAdjustedP, deltaBeta, minimumAbsoluteDeltaBeta using the field table and calculation rules, then run the tool.
- Read significant, effectQualified, dmpCall. 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 |
|---|---|---|---|
| adjustedP | Adjusted p | number | Required |
| maximumAdjustedP | Maximum adjusted p | number | Required |
| deltaBeta | Delta beta | number | Required |
| minimumAbsoluteDeltaBeta | Minimum absolute delta beta | number | Required |
Enter p/cutoff 0–1, finite signed delta and nonnegative minimum; return both gates and conjunction.
pass=p≤cutoff AND abs(deltaBeta)≥minimumEffect Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| significant | Significant | boolean |
| effectQualified | Effect qualified | boolean |
| dmpCall | DMP call | boolean |
{
"input": {
"adjustedP": 0.01,
"maximumAdjustedP": 0.05,
"deltaBeta": 0.25,
"minimumAbsoluteDeltaBeta": 0.2
},
"output": {
"significant": true,
"effectQualified": true,
"dmpCall": true
}
}Limitations and assumptions
Delta is not capped to −1…1. No statistical test or FDR correction 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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.
Alternative or Complementary methods
Use Delta Beta Effect Classifier: Classify differential methylation effect using caller-supplied beta thresholds. For a complementary task, use Probe Pvalue Filter: Exclude methylation probes failing a detection p-value threshold.
References
-
DMP Significance Gate — tool.io
Similar or alternative tools
- Delta Beta Effect Classifier
Classify differential methylation effect using caller-supplied beta thresholds.
- Probe Pvalue Filter
Exclude methylation probes failing a detection p-value threshold.