Biological Variation Coefficient

Convert negative-binomial dispersions to biological coefficients of variation.

Description

For a negative-binomial dispersion parameterization, the biological coefficient of variation is its square root.

For a negative-binomial dispersion parameterization, the biological coefficient of variation is its square root. Conversion does not estimate the dispersion from replicate counts.^[1]

Convert negative-binomial dispersions to biological coefficients of variation.

When to use Biological Variation Coefficient

Use this tool to convert negative-binomial dispersions to biological coefficients of variation.

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 Biological Variation Coefficient 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 dispersions, maximumBcv using the field table and calculation rules, then run the tool.
Read bcvs, passingIndexes, meanBcv. 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
dispersions	Dispersions	list of number	Required
maximumBcv	Maximum bcv	number	Required

Enter a nonempty nonnegative dispersion list and nonnegative maximum BCV. Return coefficients, their arithmetic mean and zero-based indices with BCV at most the maximum. Zero dispersion gives zero BCV.

BCV_i=sqrt(dispersion_i); meanBCV=mean(BCV_i)

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

Output field	Meaning	Value type
bcvs	Bcvs	list of number
passingIndexes	Passing indexes	list of number
meanBcv	Mean bcv	number

json

{
  "input": {
    "dispersions": [
      0.01,
      0.04,
      0.09
    ],
    "maximumBcv": 0.25
  },
  "output": {
    "bcvs": [
      0.1,
      0.2,
      0.3
    ],
    "passingIndexes": [
      0,
      1
    ],
    "meanBcv": 0.20000000000000004
  }
}

Limitations and assumptions

The supplied dispersions must use the intended parameterization. Mean BCV is not square root of mean dispersion; no fitting, shrinkage or significance analysis is performed.

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.

Alternative or Complementary methods

Use HVG Dispersion Selector: Select highly variable genes by variance-to-mean dispersion. For a complementary task, use Housekeeping Cv Rank: Rank housekeeping genes by replicate coefficient of variation.

References

Biological Variation Coefficient — tool.io

Similar or alternative tools

HVG Dispersion Selector
Select highly variable genes by variance-to-mean dispersion.
Housekeeping Cv Rank
Rank housekeeping genes by replicate coefficient of variation.