meQTL Cis-Window
Check variant-CpG distance against a supplied cis window.
Description
A cis-window criterion screens distance between a variant and CpG.
A cis-window criterion screens distance between a variant and CpG.1
Check variant-CpG distance against a supplied cis window.
When to use meQTL Cis-Window
Use this tool to check variant-CpG distance against a supplied cis window.
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 meQTL Cis-Window 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 variantPositionBp, cpgPositionBp, cisWindowBp using the field table and calculation rules, then run the tool.
- Read distanceBp, withinCisWindow. 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 |
|---|---|---|---|
| variantPositionBp | Variant position | number; minimum: 0 | Required |
| cpgPositionBp | CpG position | number; minimum: 0 | Required |
| cisWindowBp | Cis-window radius | number; minimum: 0 | Required |
Enter nonnegative finite positions/window and return distance/inclusive flag.
distance=abs(variantPosition−cpgPosition); pass=distance≤window Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| distanceBp | Variant-CpG distance | number; minimum: 0 |
| withinCisWindow | Within cis window | boolean |
{
"input": {
"variantPositionBp": 1000,
"cpgPositionBp": 1300,
"cisWindowBp": 500
},
"output": {
"distanceBp": 300,
"withinCisWindow": true
}
}Limitations and assumptions
Fractional positions are accepted; no chromosome match, association or linkage analysis 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 CPG Region Classifier: Classify a CpG’s distance from a caller-supplied island. For a complementary task, use TAD Boundary Distance: Measure adjacent TAD boundary distances.
References
-
meQTL Cis-Window — tool.io
Similar or alternative tools
- CPG Region Classifier
Classify a CpG’s distance from a caller-supplied island.
- TAD Boundary Distance
Measure adjacent TAD boundary distances.