Methylation Beta Value C/(C+T) Ratio Calculator
Compute bisulfite read-count beta C/(C+T); not an Illumina array beta with offsets or an m-value transform.
Description
Compute bisulfite read-count beta C/(C+T); not an Illumina array beta with offsets or an m-value transform.
A read-count methylation fraction compares methylated observations with their methylated-plus-unmethylated total. It differs from an intensity-based array beta value or a PCR cycle-threshold ratio.
When to use this tool
Compute bisulfite read-count beta C/(C+T); not an Illumina array beta with offsets or an m-value transform.
- Prepare the supplied methylatedReads, unmethylatedReads fields for this operation.
- Compare the complete example with the representation used by your own input before carrying the result into another step.
How to use the tool and how it works
- Enter methylatedReads, unmethylatedReads. Use the exact text syntax, units and index conventions explained below.
- Run the tool. If input validation fails, correct the supplied fields before interpreting any result.
- Read result.readCountBeta. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.
Validate nonnegative integer methylatedReads and unmethylatedReads with a positive combined count. Return readCountBeta=methylatedReads/(methylatedReads+unmethylatedReads), with the helper's bounded count checks.1
| Input field | Meaning and representation | Accepted input |
|---|---|---|
| methylatedReads | methylated reads. | Finite number |
| unmethylatedReads | unmethylated reads. | Integer from 0 to 1e12 inclusive |
| Output field | Interpretation |
|---|---|
| result | Object containing the named outputs below. |
| result.readCountBeta | The read count beta value under the stated formula or text convention. |
{
"input": {
"methylatedReads": 3,
"unmethylatedReads": 1
},
"output": {
"result": {
"readCountBeta": 0.75
}
}
}Limitations and assumptions
- No offset, conversion-efficiency correction or uncertainty is included. Despite the tool ID, inputs are read counts rather than Ct measurements; a zero total is rejected.
- Every declared top-level field is required and unexpected fields are rejected. Numeric inputs must be finite; ordinary text fields are bounded to 8,192 UTF-16 code units, with tighter operation-specific limits where stated.
- Ordinary string lists have at most 128 entries of at most 128 code units each; numeric lists and matrices have separate bounded size checks. Nonfinite results and excessively large serialized outputs are rejected.
- Indexes are zero-based and spans have an exclusive end unless explicitly stated otherwise. A valid false, null or empty-list result is distinct from malformed input.
Alternative or Complementary methods
Interpret computational summaries alongside assay controls and the original experimental evidence. A mark association, charge model or threshold flag does not independently establish a chromatin state, causal mechanism or transcriptional effect.
References
Similar or alternative tools
- delta beta effect classifier
Delta beta expresses signed methylation-fraction change; magnitude bands use selected cutoffs.
- dunedinpace ratio
A biological-change ratio is a supplied pace measure.