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investigate-weighted-gene

Investigate weighted gene enrichment methods

Metadata

Statusdone
Assignedagent-84
Agent identity3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3
Created2026-04-01T14:48:38.666257695+00:00
Started2026-04-01T14:50:35.368908061+00:00
Completed2026-04-01T14:53:49.757630307+00:00
Tagseval-scheduled
Eval score0.91
└ blocking impact0.90
└ completeness0.95
└ coordination overhead0.95
└ correctness0.90
└ downstream usability0.90
└ efficiency0.85
└ intent fidelity0.95
└ style adherence0.90

Description

Goal

Investigate weighted gene enrichment approaches where genes are weighted by copy number rather than treated as binary present/absent.

Specific Questions

  • How to implement GSEA with pre-ranked lists using copy number as ranking?
  • What weighted hypergeometric/Fisher test implementations exist?
  • How to handle background weighting (genome-wide gene copy counts)?
  • Available tools: weighted GSEA, custom R scripts, existing packages?

Output

  • Assessment of weighted GSEA feasibility
  • Available weighted statistical test implementations
  • Background construction requirements
  • Tool availability and implementation complexity
  • Runtime estimates for ~1,189 gene copies

Validation

  • At least 2 weighted enrichment methods evaluated
  • Implementation requirements documented
  • Background weighting approach specified

Depends on

Required by

Log