Changing Output From Gene ID to Symbol When Running findMarkers from Scran

Question

[ian.folkert]

Hi, I'm trying to use findMarkers from the Scran package to identify markers for the clusters in my SingleCellExperiment. The SingleCellExperiment objects have both Gene ID and Gene Symbols in their rowData slots. When I run the findMarkers function it works just fine, but the output only seems to contain the gene IDs, rather than the gene Symbols. I would prefer to see the gene symbols as they are easier to look at and more meaningful when plotting out results. I haven't been able to find an answer to this, but is there a way to either set the gene Symbols as the default output/rowData for the SingleCellExperiment, or to have findMarkers output only the gene Symbol? Thanks so much for your help.

[gouqiaomail]

hi, I had the same issue, did you find good way to solve this matter?

Answer 1

[ian.folkert]

The one solution I've found to this so far is to assign the gene symbols as the rownames for each object after calling read10xCounts, as below, since I don't really want any output to list the genes by Ensembl ID, but I'm sure there's probably a better way to do this.

rownames(sce.leuk.dmso) <- rowData(sce.leuk.dmso)$Symbol