Imprinting DMR Parent-of-Origin Allele Skew Detector

Retain parental direction in independently phased allele expression skew; imbalance is not proof of imprinting or loss of imprinting.

Description

Retain parental direction in independently phased allele expression skew; imbalance is not proof of imprinting or loss of imprinting.

A parent-of-origin expression imbalance can be quantified before its cause is interpreted. A caller-selected skew threshold screens that imbalance without proving imprinting.

When to use this tool

Retain parental direction in independently phased allele expression skew; imbalance is not proof of imprinting or loss of imprinting.

Prepare the supplied maternalExpression, paternalExpression, callerSkewFraction 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 maternalExpression, paternalExpression, callerSkewFraction. 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.fractionMaternal, result.dominantParent, result.skewed, result.imprintingEstablished. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.

Require nonnegative maternal/paternal expression with a positive sum and callerSkewFraction from 0.5 through 1. Compute the maternal fraction, label the larger parental contribution or tie, and flag when either parent's fraction meets the supplied threshold.^[1]

Input field	Meaning and representation	Accepted input
maternalExpression	maternal expression.	Finite number; greater than zero; zero or greater
paternalExpression	paternal expression.	Finite number; zero or greater
callerSkewFraction	caller skew fraction.	Finite number

Output field	Interpretation
result	Object containing the named outputs below.
result.fractionMaternal	The fraction maternal value under the stated formula or text convention.
result.dominantParent	The dominant parent value under the stated formula or text convention.
result.skewed	Flag for skewed under the exact condition described above.
result.imprintingEstablished	Flag for imprinting established under the exact condition described above.

json

{
  "input": {
    "maternalExpression": 9,
    "paternalExpression": 1,
    "callerSkewFraction": 0.8
  },
  "output": {
    "result": {
      "fractionMaternal": 0.9,
      "dominantParent": "maternal",
      "skewed": true,
      "imprintingEstablished": false
    }
  }
}

Limitations and assumptions

imprintingEstablished is always false. Ratios do not account for mapping bias, allele dosage or uncertainty; at the threshold 0.5, even an equal contribution meets the screen.
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

Tool behavior and example: Imprinting DMR Parent-of-Origin Allele Skew Detector — tool.io

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