XY Intensity Classifier
Classify X/Y intensity contrast without inferring an individual’s gender.
Description
X/Y intensity contrast is a coarse array-signal comparison, distinct from a karyotype.
X/Y intensity contrast is a coarse array-signal comparison, distinct from a karyotype.1
Classify X/Y intensity contrast without inferring an individual’s gender.
When to use XY Intensity Classifier
Use this tool to classify X/Y intensity contrast without inferring an individual’s gender.
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 XY Intensity Classifier 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 xIntensity, yIntensity, minimumLog2Contrast using the field table and calculation rules, then run the tool.
- Read log2Contrast, predictedClass, confident. 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 |
|---|---|---|---|
| xIntensity | X intensity | number | Required |
| yIntensity | Y intensity | number | Required |
| minimumLog2Contrast | Minimum log 2 contrast | number | Required |
Enter positive intensities and a nonnegative cutoff. Return log2 contrast and confidence. If confidence fails, predictedClass is undetermined; otherwise positive contrast gives x-dominant and zero/negative contrast gives y-dominant.
contrast=log2(X/Y); confident=abs(contrast)≥threshold Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| log2Contrast | Log 2 contrast | number |
| predictedClass | Predicted class | string; one of "x-dominant", "y-dominant", "undetermined" |
| confident | Confident | boolean |
{
"input": {
"xIntensity": 800,
"yIntensity": 200,
"minimumLog2Contrast": 1
},
"output": {
"log2Contrast": 2,
"predictedClass": "x-dominant",
"confident": true
}
}Limitations and assumptions
Zero contrast is labeled y-dominant even with cutoff zero. No chromosome complement or clinical classification is established.
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 X-Inactivation Skew: Classify X-inactivation skew from allele counts. For a complementary task, use XCI Escapee Discordance: Flag XCI escapee candidates with expression skew but balanced methylation.
References
-
XY Intensity Classifier — tool.io
Similar or alternative tools
- X-Inactivation Skew
Classify X-inactivation skew from allele counts.
- XCI Escapee Discordance
Flag XCI escapee candidates with expression skew but balanced methylation.