DeseqStats for a single gene of interest
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Description
Hello
Is there a way to restrict DeseqStats (Wald test) to only one specific gene instead of the entire DeseqDataSet?
I am performing genetic interaction testing across 100,000+ contexts (Gene-SNP-Celltype). For each test, I only need the summary statistics for a single target gene.
I have already run dds.deseq2() on the full dataset, but running DeseqStats(dds, ...).summary() on all genes is computationally prohibitive at this scale. I have tried subsetting the dds object to the gene of interest before calling DeseqStats, but this does not work.
Is there a recommended way to perform the Wald test and results extraction for a single gene to optimize runtime?
i am using (pydeseq2.version) 0.5.4
thanks
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Research direction
Start with the DeseqStats entry point and the dds.deseq2() results path in PyDESeq2 0.5.4; compare how a full DeseqDataSet is handled with the attempted single-gene subset. Define done as obtaining Wald-test summary statistics for one target gene without processing all genes, while preserving the existing full-dataset behavior.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100