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research-r-alternatives

Research R alternatives to phyper() for weighted testing

Metadata

Statusdone
Assignedagent-127
Agent identity3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3
Created2026-04-01T15:01:16.126775262+00:00
Started2026-04-01T15:06:37.253470366+00:00
Completed2026-04-01T15:13:50.107629092+00:00
Tagseval-scheduled
Eval score0.89
└ blocking impact0.95
└ completeness0.92
└ coordination overhead0.92
└ correctness0.95
└ downstream usability0.85
└ efficiency0.88
└ intent fidelity0.97
└ style adherence0.90

Description

Research alternative R functions and packages that could be used for copy-number weighted hypergeometric testing. Evaluate existing implementations and identify potential improvements.

R Functions to Investigate:

  • dhyper(), qhyper(), rhyper() family
  • fisher.test() and its weighted variants
  • Custom hypergeometric implementations in CRAN packages
  • BioConductor enrichment analysis tools
  • Permutation-based alternatives

Packages to Review:

  • stats (base R hypergeometric functions)
  • BioConductor GOstats, clusterProfiler
  • CRAN packages for enrichment analysis
  • Weighted statistical testing packages

Evaluation Criteria:

  • Support for weighted/instance-based testing
  • Computational efficiency
  • Statistical robustness
  • API usability and integration

Expected Outputs:

  • Comparative analysis of R implementations
  • Recommendations for best R approach
  • Gap analysis for missing functionality
  • Integration strategy recommendations

Depends on

Required by

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