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
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