Tumor Normal Copy Ratio
Interpret log2 tumor/normal ratios with an explicit normal-cell admixture and baseline ploidy model.
Description
Tumor/normal copy ratios mix tumor cells with normal cells.
Tumor/normal copy ratios mix tumor cells with normal cells. Purity determines how strongly observed ratios differ from the tumor copy-number state.1
Interpret log2 tumor/normal ratios with an explicit normal-cell admixture and baseline ploidy model.
When to use Tumor Normal Copy Ratio
Use this for the following task: Interpret log2 tumor/normal ratios with an explicit normal-cell admixture and baseline ploidy model.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Tumor Normal Copy Ratio 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 log2Ratios, normalPloidy, purityFraction using the field table, then run the tool.
- Read observedCopyRatios, tumorCopyNumbers. 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 |
|---|---|---|---|
| log2Ratios | Log2 sample-to-normal ratios in the simple admixture model R = purity * tumorCopies / normalPloidy + (1 - purity). | list of number; minimum entries 0; maximum entries 100000; each entry: number | Required |
| normalPloidy | Normal ploidy | number; greater than 0 | Required |
| purityFraction | Purity fraction | number; greater than 0; maximum 1 | Required |
Require a positive baseline ploidy and purity in (0,1]. Transform each log ratio and invert the admixture model, using stable near-zero calculations. Reject incompatible negative copy numbers or nonfinite results.2
ratio = 2^log2Ratio; tumorCopies = normalPloidy[1 + (ratio−1)/purity] This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| observedCopyRatios | Observed copy ratios | list of number |
| tumorCopyNumbers | Tumor copy numbers | list of number |
{
"input": {
"log2Ratios": [
-1,
0,
1
],
"normalPloidy": 2,
"purityFraction": 1
},
"output": {
"observedCopyRatios": [
0.5,
1,
2
],
"tumorCopyNumbers": [
1,
2,
4
]
}
}Limitations and assumptions
The inferred copy numbers are continuous model values. Heterogeneity, subclonality and baseline normalization must be assessed separately.
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 Purity Ploidy Grid Fit for this operation: Choose the minimum-residual cell from an externally fitted purity-by-ploidy grid. For a complementary task, use Loh Segments for this operation: Merge contiguous segments meeting a supplied minor-allele copy-number LOH criterion.
Further background: Background specification: Tumor Normal Copy Ratio.
References
-
Tumor Normal Copy Ratio — tool.io
Similar or alternative tools
- Purity Ploidy Grid Fit
Choose the minimum-residual cell from an externally fitted purity-by-ploidy grid.
- Loh Segments
Merge contiguous segments meeting a supplied minor-allele copy-number LOH criterion.