Copy Number Switches
Count copy-number state switches as an oscillation feature, not a chromothripsis diagnosis.
Description
Copy-number state changes provide an oscillation feature along ordered segments.
Copy-number state changes provide an oscillation feature along ordered segments. Alternation between two states is descriptive evidence, not a diagnosis.
Count copy-number state switches as an oscillation feature, not a chromothripsis diagnosis.
When to use Copy Number Switches
Use this for the following task: Count copy-number state switches as an oscillation feature, not a chromothripsis diagnosis.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Copy Number Switches and understand its results
- Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
- Enter copyNumberStates using the field table, then run the tool.
- Read switchCount, distinctStates, twoStateOscillation. Interpret flags, units, ordering and placeholder values using the rules below.
- Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.
| Input field | Meaning | Value type and bounds | Requirement |
|---|---|---|---|
| copyNumberStates | Copy number states | list of integer; minimum entries 1; maximum entries 100000; each entry: integer; minimum 0 | Required |
Supply supported nonnegative integer states in genomic order. Count adjacent changes and distinct values, then apply the stated flag rule.1
switches = adjacent unequal states; twoStateOscillation = distinctStates == 2 AND switches ≥ 2 This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| switchCount | Switch count | integer |
| distinctStates | Distinct states | integer |
| twoStateOscillation | Exactly two supplied states and at least two switches; consecutive equal states do not switch. | boolean |
{
"input": {
"copyNumberStates": [
1,
2,
1,
2,
2,
1
]
},
"output": {
"switchCount": 4,
"distinctStates": 2,
"twoStateOscillation": true
}
}Limitations and assumptions
Repeated adjacent states are allowed. Segment sizes and breakpoints are absent, and chromothripsis is not diagnosed.
The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.
Alternative or Complementary methods
Choose Loh Segments for this operation: Merge contiguous segments meeting a supplied minor-allele copy-number LOH criterion. For a complementary task, use Genomic Scar Composite for this operation: Combine supplied LOH, telomeric imbalance, and large-transition counts with explicit weights; not a clinical HRD test.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Copy Number Switches — tool.io
Similar or alternative tools
- Loh Segments
Merge contiguous segments meeting a supplied minor-allele copy-number LOH criterion.
- Genomic Scar Composite
Combine supplied LOH, telomeric imbalance, and large-transition counts with explicit weights; not a clinical HRD test.