Signed Dprime

Normalize signed linkage disequilibrium D by its sign-specific feasible maximum.

Description

Linkage disequilibrium D measures departure from independent allele occurrence.

Linkage disequilibrium D measures departure from independent allele occurrence. Signed D-prime divides by the feasible maximum appropriate to D’s sign.

Normalize signed linkage disequilibrium D by its sign-specific feasible maximum.

When to use Signed Dprime

Use this for the following task: Normalize signed linkage disequilibrium D by its sign-specific feasible maximum.

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.

How to use Signed Dprime and understand its results

Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
Enter firstAlleleFrequency, secondAlleleFrequency, jointHaplotypeFrequency using the field table, then run the tool.
Read linkageD, dMaximum, dprime. 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
firstAlleleFrequency	First allele frequency	number	Required
secondAlleleFrequency	Second allele frequency	number	Required
jointHaplotypeFrequency	Joint haplotype frequency	number	Required

Require frequencies in [0,1] and a joint frequency compatible with both marginals. Preserve sign in D/Dmax and reject a zero normalization denominator.^[1]

D = haplotypeFrequency−pq; Dmax = min(p(1−q),(1−p)q) if D≥0, otherwise min(pq,(1−p)(1−q))

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
linkageD	Linkage d	number
dMaximum	D maximum	number
dprime	Dprime	number

json

{
  "input": {
    "firstAlleleFrequency": 0.5,
    "secondAlleleFrequency": 0.5,
    "jointHaplotypeFrequency": 0.4
  },
  "output": {
    "linkageD": 0.15000000000000002,
    "dMaximum": 0.25,
    "dprime": 0.6000000000000001
  }
}

Limitations and assumptions

Fixed marginal alleles make D-prime undefined here. This does not calculate r squared or estimate frequencies from genotypes.

The tool evaluates supplied observations or a declared model. It does not establish the biological cause of an observed pattern. 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 Solid Spine Haplotype Block for this operation: Extend a solid-spine block from the first SNP while both boundary SNPs retain caller-required linkage with all enclosed SNPs. For a complementary task, use Population FST for this operation: Compute heterozygosity-based FST from population allele frequencies and explicit weights.

The implementation reference documents the exact calculation, supported input shapes and returned fields.

References

Signed Dprime — tool.io

Similar or alternative tools

Solid Spine Haplotype Block
Extend a solid-spine block from the first SNP while both boundary SNPs retain caller-required linkage with all enclosed SNPs.
Population FST
Compute heterozygosity-based FST from population allele frequencies and explicit weights.