Question: Changing Output From Gene ID to Symbol When Running findMarkers from Scran
0
gravatar for ian.folkert
10 weeks ago by
ian.folkert0 wrote:

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.

rna-seq R single-cell rna-seq • 133 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by ian.folkert0
0
gravatar for ian.folkert
10 weeks ago by
ian.folkert0 wrote:

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
ADD COMMENTlink written 10 weeks ago by ian.folkert0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1913 users visited in the last hour