Perform Quality Control on a List of Protein Complexes

A diagnostic tool to assess complex size distribution and distinguish between true redundancy (synonyms) and biological hierarchy (subsets).

Usage

qcComplexList(
  complexList,
  redundancyThreshold = 0.9,
  subsetThreshold = 0.9,
  verbose = TRUE
)

Arguments

complexList

A list of character vectors (protein complexes).

redundancyThreshold

Threshold for Jaccard similarity warning. Defaults to 0.9.

subsetThreshold

Threshold for Simpson coefficient (subset) reporting. Defaults to 0.9.

verbose

Logical.

Value

Invisibly returns the input `complexList`.

Details

**Systems Biology Rationale:** To maintain a diverse functional landscape, it is critical to distinguish between two types of similarity:

1. **Jaccard Similarity (Redundancy):** Complex A and B are nearly identical. * *Action:* Merge these (using `refineComplexList`). 2. **Overlap/Simpson Similarity (Hierarchy):** Complex A is a subset of Complex B. * *Action:* **Keep these.** Do not merge. These often represent distinct biological states (e.g., Core Complex vs. Holo-Complex).

This report calculates both metrics to guide your refinement strategy.

Author

Qingzhou Zhang <zqzneptune@hotmail.com>