X-Inactivation Skew
Classify X-inactivation skew from allele counts.
Description
X-inactivation skew summarizes the imbalance between two observed cell populations.
X-inactivation skew summarizes the imbalance between two observed cell populations.1
Classify X-inactivation skew from allele counts.
When to use X-Inactivation Skew
Use this tool to classify X-inactivation skew from allele counts.
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 X-Inactivation Skew 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 alleleOneCells, alleleTwoCells, skewThresholdPercent using the field table and calculation rules, then run the tool.
- Read majorAllelePercent, skewRatio, skewed. 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 |
|---|---|---|---|
| alleleOneCells | Allele-one active cells | integer; minimum: 0 | Required |
| alleleTwoCells | Allele-two active cells | integer; minimum: 0 | Required |
| skewThresholdPercent | Skew threshold | number; minimum: 50; maximum: 100 | Required |
Enter nonnegative integer counts with positive total and threshold 50–100%. Return majorAllelePercent, skewRatio and inclusive skewed flag; minor share is used internally rather than returned.
major%=100max(counts)/sum(counts) Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| majorAllelePercent | Major allele share | number; minimum: 50; maximum: 100 |
| skewRatio | Major-minor ratio | number; minimum: 1 |
| skewed | Skewed | boolean |
{
"input": {
"alleleOneCells": 80,
"alleleTwoCells": 20,
"skewThresholdPercent": 75
},
"output": {
"majorAllelePercent": 80,
"skewRatio": 4,
"skewed": true
}
}Limitations and assumptions
Zero minor count returns major count as a finite skew-ratio placeholder. No tissue-specific 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 XCI Escapee Discordance: Flag XCI escapee candidates with expression skew but balanced methylation. For a complementary task, use XY Intensity Classifier: Classify X/Y intensity contrast without inferring an individual’s gender.
References
-
X-Inactivation Skew — tool.io
Similar or alternative tools
- XCI Escapee Discordance
Flag XCI escapee candidates with expression skew but balanced methylation.
- XY Intensity Classifier
Classify X/Y intensity contrast without inferring an individual’s gender.