Imprinting Loss
Flag loss of imprinting from biallelic expression.
Description
A minor-allele share is one screening dimension for loss-of-imprinting review.
A minor-allele share is one screening dimension for loss-of-imprinting review.1
Flag loss of imprinting from biallelic expression.
When to use Imprinting Loss
Use this tool to flag loss of imprinting from biallelic expression.
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 Imprinting Loss 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 maternalExpression, paternalExpression, minorThresholdPercent using the field table and calculation rules, then run the tool.
- Read minorAllelePercent, lossOfImprinting. 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 |
|---|---|---|---|
| maternalExpression | Maternal expression | number; minimum: 0 | Required |
| paternalExpression | Paternal expression | number; minimum: 0 | Required |
| minorThresholdPercent | Minor allele threshold | number; minimum: 0; maximum: 50 | Required |
Enter nonnegative signals with positive sum and cutoff 0–50. Return share and inclusive flag.
minor%=100min(maternal,paternal)/sum Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| minorAllelePercent | Minor allele share | number; minimum: 0; maximum: 50 |
| lossOfImprinting | Loss of imprinting | boolean |
{
"input": {
"maternalExpression": 80,
"paternalExpression": 20,
"minorThresholdPercent": 15
},
"output": {
"minorAllelePercent": 20,
"lossOfImprinting": true
}
}Limitations and assumptions
Cutoff zero flags even zero minor signal. No parent-of-origin, tissue reference or diagnosis 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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.
Alternative or Complementary methods
Use Allele–Methylation Coupling: Detect allele-specific methylation from phased read counts. For a complementary task, use X-Inactivation Skew: Classify X-inactivation skew from allele counts.
References
-
Imprinting Loss — tool.io
Similar or alternative tools
- Allele–Methylation Coupling
Detect allele-specific methylation from phased read counts.
- X-Inactivation Skew
Classify X-inactivation skew from allele counts.