investigate-permutation-based

Metadata

Status	done
Assigned	`agent-79`
Agent identity	`3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3`
Created	2026-04-01T14:48:45.290025388+00:00
Started	2026-04-01T14:50:32.886124914+00:00
Completed	2026-04-01T14:54:04.251647204+00:00
Tags	`eval-scheduled`
Eval score	0.88
└ blocking impact	0.92
└ completeness	0.93
└ coordination overhead	0.90
└ correctness	0.87
└ downstream usability	0.83
└ efficiency	0.85
└ intent fidelity	0.91
└ style adherence	0.88

Description

Goal

Investigate permutation-based null distribution approach using random genomic interval sampling.

Specific Questions

How to implement bedtools shuffle for subtelomeric regions?
What constraints for random sampling (same sizes, subtelomeric only)?
Computational feasibility of 10,000 permutations?
How to count gene copies per GO term in each permutation?
Statistical framework for comparing observed vs null distributions?

Output

Detailed permutation protocol design
Computational resource requirements (time/memory)
Statistical testing approach for null comparison
Implementation complexity assessment
Precedent for this approach in genomics literature

Validation

Permutation protocol clearly specified
Resource requirements quantified
Statistical framework documented

## Goal
Investigate permutation-based null distribution approach using random genomic interval sampling.

## Specific Questions
- How to implement bedtools shuffle for subtelomeric regions?
- What constraints for random sampling (same sizes, subtelomeric only)?
- Computational feasibility of 10,000 permutations?
- How to count gene copies per GO term in each permutation?
- Statistical framework for comparing observed vs null distributions?

## Output
- Detailed permutation protocol design
- Computational resource requirements (time/memory)  
- Statistical testing approach for null comparison
- Implementation complexity assessment
- Precedent for this approach in genomics literature

## Validation
- Permutation protocol clearly specified
- Resource requirements quantified
- Statistical framework documented

Depends on

Required by

done synthesize-findings-and

Log

2026-04-01T14:50:32.886126096+00:00 Spawned by coordinator --executor claude --model claude-sonnet-4-20250514
2026-04-01T14:50:51.757191930+00:00 Starting permutation-based enrichment investigation - will analyze bedtools shuffle, statistical frameworks, and computational requirements
2026-04-01T14:51:22.643705884+00:00 Analyzed project context: 29 PHR intervals, 220 genes total, 23 protein-coding genes showing olfactory receptor enrichment (p=0.029). Starting permutation approach investigation.
2026-04-01T14:53:41.874563886+00:00 Completed comprehensive permutation analysis investigation - created detailed protocol with implementation details, resource requirements, and statistical framework
2026-04-01T14:53:59.709105766+00:00 Validated: ✓ Permutation protocol clearly specified (bedtools shuffle with constraints), ✓ Resource requirements quantified (5.5-8.5h, <2GB RAM), ✓ Statistical framework documented (empirical p-values, effect sizes)
2026-04-01T14:54:04.251651202+00:00 Task marked as done