Cell Fraction Constraint

Check deconvolved cell fractions sum to one within tolerance.

Description

Deconvolved fractions should often sum to one while each lies between zero and one.

Deconvolved fractions should often sum to one while each lies between zero and one. A numerical closure check is independent of whether the estimated composition is biologically plausible.^[1]

Check deconvolved cell fractions sum to one within tolerance.

When to use Cell Fraction Constraint

Use this tool to check deconvolved cell fractions sum to one within tolerance.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use Cell Fraction Constraint and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter cellFractions, sumTolerance using the field table and calculation rules, then run the tool.
Read sum, deviation, valid. 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
cellFractions	Cell fractions	list of number	Required
sumTolerance	Sum tolerance	number	Required

Enter a nonempty list of fractions in 0–1 and nonnegative sum tolerance. Return sum, absolute deviation and an inclusive valid flag. Values are not automatically renormalized.

sum=Σfractions; deviation=|sum−1|; valid=deviation≤tolerance

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
sum	Sum	number
deviation	Deviation	number
valid	Valid	boolean

json

{
  "input": {
    "cellFractions": [
      0.2,
      0.3,
      0.5
    ],
    "sumTolerance": 0.001
  },
  "output": {
    "sum": 1,
    "deviation": 0,
    "valid": true
  }
}

Limitations and assumptions

This does not estimate fractions, check identifiability or validate a signature matrix. A large chosen tolerance may accept poor closure, and arithmetic validity does not establish accuracy.

Numeric inputs 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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use Tumor Purity Proxy: Compute a caller-supplied marker-based tumor purity proxy, not a clinical ESTIMATE score. For a complementary task, use Immune Signature Score: Score immune-cell signature enrichment from standardized gene expression.

References

Cell Fraction Constraint — tool.io

Similar or alternative tools

Tumor Purity Proxy
Compute a caller-supplied marker-based tumor purity proxy, not a clinical ESTIMATE score.
Immune Signature Score
Score immune-cell signature enrichment from standardized gene expression.