Purity Ploidy Grid Fit
Choose the minimum-residual cell from an externally fitted purity-by-ploidy grid.
Description
Purity/ploidy fitting can yield several candidate cells with residual scores.
Purity/ploidy fitting can yield several candidate cells with residual scores. Selecting the lowest score summarizes an externally computed grid.
Choose the minimum-residual cell from an externally fitted purity-by-ploidy grid.
When to use Purity Ploidy Grid Fit
Use this for the following task: Choose the minimum-residual cell from an externally fitted purity-by-ploidy grid.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Purity Ploidy Grid Fit 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 purityValues, ploidyValues, residualGrid using the field table, then run the tool.
- Read bestPurity, bestPloidy, minimumResidual. 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 |
|---|---|---|---|
| purityValues | Purity values | list of number; minimum entries 1; maximum entries 128; each entry: number; minimum 0; maximum 1 | Required |
| ploidyValues | Ploidy values | list of number; minimum entries 1; maximum entries 128; each entry: number; greater than 0 | Required |
| residualGrid | Residual grid | list of list of number; minimum entries 1; maximum entries 128; each entry: list of number; minimum entries 1; maximum entries 128; each entry: number; minimum 0 | Required |
Use a rectangular grid with rows matching purity values in [0,1] and columns matching positive ploidies. Scan in row-major order and update only for a strictly lower residual.1
best cell = first row-major minimum residual This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| bestPurity | Best purity | number |
| bestPloidy | Best ploidy | number |
| minimumResidual | Minimum residual | number |
{
"input": {
"purityValues": [
0.5,
1
],
"ploidyValues": [
2,
3
],
"residualGrid": [
[
4,
2
],
[
1,
3
]
]
},
"output": {
"bestPurity": 1,
"bestPloidy": 2,
"minimumResidual": 1
}
}Limitations and assumptions
The tool does not fit the grid, constrain residuals to a particular statistical meaning or estimate uncertainty.
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 Tumor Normal Copy Ratio for this operation: Interpret log2 tumor/normal ratios with an explicit normal-cell admixture and baseline ploidy model. 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
-
Purity Ploidy Grid Fit — tool.io
Similar or alternative tools
- Tumor Normal Copy Ratio
Interpret log2 tumor/normal ratios with an explicit normal-cell admixture and baseline ploidy model.
- Genomic Scar Composite
Combine supplied LOH, telomeric imbalance, and large-transition counts with explicit weights; not a clinical HRD test.