WGCNA Power Selector

Select the first WGCNA power meeting a caller-supplied scale-free-fit criterion.

Description

Soft-threshold power screening can use previously measured scale-free fit values.

Soft-threshold power screening can use previously measured scale-free fit values. Selecting a qualifying tested power is separate from calculating a network or fitting its degree distribution.^[1]

Select the first WGCNA power meeting a caller-supplied scale-free-fit criterion.

When to use WGCNA Power Selector

Use this tool to select the first WGCNA power meeting a caller-supplied scale-free-fit criterion.

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 WGCNA Power Selector 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 powers, scaleFreeR2, minimumR2 using the field table and calculation rules, then run the tool.
Read selectedPower, selectedR2, qualifiedPowers. 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
powers	Powers	list of number	Required
scaleFreeR2	Scale free r 2	list of number	Required
minimumR2	Minimum r 2	number	Required

Enter aligned nonempty powers and R² values within 0–1. Keep the intended search order: the tool returns the first qualifying power, its R² and all qualifying powers in input order. No qualifying value is an input error.

selected=first supplied power whose R²≥minimumR2

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

Output field	Meaning	Value type
selectedPower	Selected power	number
selectedR2	Selected r 2	number
qualifiedPowers	Qualified powers	list of number

json

{
  "input": {
    "powers": [
      2,
      4,
      6
    ],
    "scaleFreeR2": [
      0.5,
      0.8,
      0.85
    ],
    "minimumR2": 0.8
  },
  "output": {
    "selectedPower": 4,
    "selectedR2": 0.8,
    "qualifiedPowers": [
      4,
      6
    ]
  }
}

Limitations and assumptions

The powers are not sorted and positivity/integer power constraints are not separately enforced. The finite criterion is caller supplied; this does not compute WGCNA fit or assess connectivity tradeoffs.

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 TOM Symmetry Audit: Audit topological-overlap matrix symmetry and diagonal entries. For a complementary task, use Hub Gene Rank: Rank module genes by supplied eigengene connectivity.

References

WGCNA Power Selector — tool.io

Similar or alternative tools

TOM Symmetry Audit
Audit topological-overlap matrix symmetry and diagonal entries.
Hub Gene Rank
Rank module genes by supplied eigengene connectivity.