Epimutation Rate
Estimate epimutation rate per site and generation.
Description
Epimutation rate normalizes recorded gain/loss events by sites and generations.
Epimutation rate normalizes recorded gain/loss events by sites and generations.1
Estimate epimutation rate per site and generation.
When to use Epimutation Rate
Use this tool to estimate epimutation rate per site and generation.
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 Epimutation Rate 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 gainEvents, lossEvents, assayedSites, generations using the field table and calculation rules, then run the tool.
- Read totalEpimutations, ratePerSiteGeneration. 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 |
|---|---|---|---|
| gainEvents | Methylation gains | integer; minimum: 0 | Required |
| lossEvents | Methylation losses | integer; minimum: 0 | Required |
| assayedSites | Assayed sites | integer; minimum: 1 | Required |
| generations | Generations | integer; minimum: 1 | Required |
Enter nonnegative integer events and positive integer sites/generations; return total/rate.
rate=(gains+losses)/(sites×generations) Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| totalEpimutations | Total epimutations | integer; minimum: 0 |
| ratePerSiteGeneration | Rate per site-generation | number; minimum: 0 |
{
"input": {
"gainEvents": 30,
"lossEvents": 20,
"assayedSites": 1000,
"generations": 5
},
"output": {
"totalEpimutations": 50,
"ratePerSiteGeneration": 0.01
}
}Limitations and assumptions
Events are not capped at the denominator, so rate can exceed one. No mutation calling or uncertainty 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 Generation Skip: Count generations between exposure and observed effect. For a complementary task, use Passive Demethylation: Model passive methylation dilution across divisions.
References
-
Epimutation Rate — tool.io
Similar or alternative tools
- Generation Skip
Count generations between exposure and observed effect.
- Passive Demethylation
Model passive methylation dilution across divisions.