investigate-copy-number

Metadata

Status	done
Assigned	`agent-83`
Agent identity	`3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3`
Created	2026-04-01T14:48:51.699938176+00:00
Started	2026-04-01T14:50:33.082440329+00:00
Completed	2026-04-01T14:59:02.835885703+00:00
Tags	`eval-scheduled`
Eval score	0.90
└ blocking impact	0.95
└ completeness	0.90
└ coordination overhead	0.92
└ correctness	0.85
└ downstream usability	0.88
└ efficiency	0.90
└ intent fidelity	0.97
└ style adherence	0.95

Description

Goal

Investigate custom over-representation analysis (ORA) that weights by copy number rather than unique gene symbols.

Specific Questions

How to build custom background with genome-wide gene copy counts?
Implementation using R's phyper() function for weighted hypergeometric tests?
Input format: 1,189 gene instances vs 23 unique symbols?
How to handle gene family definitions and copy counting?
Comparison to standard ORA - what changes in the statistics?

Output

Custom weighted ORA implementation approach
Background construction methodology
Statistical framework and test modifications
Expected differences from standard ORA results
Implementation complexity and runtime estimates

Validation

Weighted hypergeometric test approach specified
Background construction protocol documented
Implementation steps clearly outlined

## Goal
Investigate custom over-representation analysis (ORA) that weights by copy number rather than unique gene symbols.

## Specific Questions
- How to build custom background with genome-wide gene copy counts?
- Implementation using R's phyper() function for weighted hypergeometric tests?
- Input format: 1,189 gene instances vs 23 unique symbols?
- How to handle gene family definitions and copy counting?
- Comparison to standard ORA - what changes in the statistics?

## Output
- Custom weighted ORA implementation approach
- Background construction methodology
- Statistical framework and test modifications
- Expected differences from standard ORA results
- Implementation complexity and runtime estimates

## Validation
- Weighted hypergeometric test approach specified
- Background construction protocol documented  
- Implementation steps clearly outlined

Depends on

Required by

Log

2026-04-01T14:50:32.799447772+00:00 Lightweight assignment: agent=Default Evaluator (31847164), exec_mode=light, context_scope=task, reason=This investigation task requires evaluating the feasibility and methodology of copy-number-weighted ORA; Evaluator's strong track record (0.91, 69 tasks) and balanced tradeoff suit research and assessment work over exploration or creation.
2026-04-01T14:50:33.082441482+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
2026-04-01T14:50:57.199462821+00:00 Starting investigation of copy-number-weighted ORA approaches
2026-04-01T14:51:38.020201477+00:00 Examined data structure: 1,189 total gene instances from 23 unique symbols with copy numbers ranging 1-39. Current ORA treats all genes equally.
2026-04-01T14:52:09.355270594+00:00 Decomposed investigation into 4 parallel subtasks: weighted background construction, R phyper() modifications, existing tools survey, and statistical framework analysis. Created integration task.
2026-04-01T14:52:31.506141719+00:00 Starting detailed investigation of custom background construction for copy-number-weighted ORA
2026-04-01T14:58:48.975167133+00:00 Investigation complete. Created comprehensive analysis covering: background construction, R phyper() modifications, input format implications, gene family strategies, statistical framework changes, and implementation synthesis. Generated 6 detailed documents with actionable recommendations.
2026-04-01T14:58:59.459853348+00:00 Validated: All task requirements met - weighted hypergeometric approach specified, background construction documented, implementation steps outlined with complexity estimates and timeline
2026-04-01T14:59:02.835887757+00:00 Task marked as done