Regulator Triad Coverage
Audit writer, eraser, and reader regulator coverage.
Description
Epigenetic writer, reader and eraser roles organize regulator evidence.
Epigenetic writer, reader and eraser roles organize regulator evidence. Presence of a label is separate from activity or causal function.1
Audit writer, eraser, and reader regulator coverage.
When to use Regulator Triad Coverage
Use this tool to audit writer, eraser, and reader regulator coverage.
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 Regulator Triad Coverage 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 requiredRegulatorClasses, presentRegulatorClasses using the field table and calculation rules, then run the tool.
- Read coveragePercent, matched, missing, unexpected. 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 |
|---|---|---|---|
| requiredRegulatorClasses | Required regulator classes | list of string | Required |
| presentRegulatorClasses | Present regulator classes | list of string | Required |
Enter requiredRegulatorClasses as the nonempty expected list and presentRegulatorClasses as observations, which may be empty. Trim entries, compare case-insensitively using en-US lowercase and collapse duplicates. Return matched/missing expected labels and unexpected observed labels. Output follows first occurrence order with the last duplicate’s trimmed spelling.
coverage%=100matchedUnique/expectedUnique Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| coveragePercent | Coverage (%) | number; minimum: 0; maximum: 100 |
| matched | Matched items | list of string |
| missing | Missing items | list of string |
| unexpected | Unexpected items | list of string |
{
"input": {
"requiredRegulatorClasses": [
"writer",
"eraser",
"reader"
],
"presentRegulatorClasses": [
"writer",
"reader"
]
},
"output": {
"coveragePercent": 66.66666666666666,
"matched": [
"writer",
"reader"
],
"missing": [
"eraser"
],
"unexpected": []
}
}Limitations and assumptions
No regulator activity, expression or mechanism is established. Blank entries are errors; requirements are entirely caller-supplied and items have equal weight.
Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use TET Cascade Stage: Map a cytosine modification to its TET cascade stage. For a complementary task, use Promoter–Enhancer State: Resolve promoter-enhancer state from H3K4 methylation signals.
References
-
Regulator Triad Coverage — tool.io
Similar or alternative tools
- TET Cascade Stage
Map a cytosine modification to its TET cascade stage.
- Promoter–Enhancer State
Resolve promoter-enhancer state from H3K4 methylation signals.