Closed kmaynard12 closed 1 year ago
@abspangler13 where where you doing this and how are along are you?
I performed it for the k= 9 data set against all of the datasets from the pilot study and two new datasets that I added. Here's the code for the two new datasets I added as well as some comments about two sets we were interested in adding. https://github.com/LieberInstitute/spatialDLPFC/blob/ea6c27cc88a374c314ccdad60303b28752964cfc/code/analysis/10_Clinical_Gene_Set_Enrichment/01_Clinical_Gene_Set_Enrichment.R#L251-L306
@kmaynard12 is going to work on this. @lahuuki, I wrote https://github.com/LieberInstitute/spatialDLPFC/tree/main/code/analysis/10_clinical_gene_set_enrichment in such a way that you would need to make 2 new scripts. One for extracting the gene IDs (ENSEMBL IDs) from the different tables @kmaynard12 will select, then another one for computing the odds ratio + making the heatmaps.
@kmaynard12 are there other case/control snRNA-seq datasets beyond the PEC ones we should be looking at?
Related to https://jhu-genomics.slack.com/archives/C01EA7VDJNT/p1673285746357859
@lahuuki I think that we can close this issue, right?