Open galaxyeee opened 1 year ago
Hm. Well, nothing particular comes to mind; everything seems to work in the following example.
library(scRNAseq)
sce <- ZeiselBrainData()
colLabels(sce) <- sce$level1class
library(scuttle)
sce <- logNormCounts(sce) # to get some log-counts
genes <- !grepl(pattern = "^Rp[l|s]|Mt", x = rownames(sce))
res <- scoreMarkers(sce, subset.row = genes)
It seems that, for some reason, S4Vectors::match
is not being properly imported, leading to the observed error. No idea why, as I very explicitly import that match
function when loading scran. I'd suggest two experiments:
brca.sce
to file with saveRDS()
, load it in a new session with readRDS()
, and see if scoreMarkers
works there. This will determine whether other packages like Seurat (or its dependencies) are interfering with my imports.library(S4Vectors)
and see if scoreMarkers
works. This will force S4Vectors::match
into the global namespace, so maybe it might get picked up inside scoreMarkers
. Maybe.Hi, @LTLA Thanks to you, I solved problem! Thank you.
Best, EUNHA
Hi @galaxyeee , I'm having the same problem, I have tried both solutions that @LTLA gives to you but can't solve it. Please, could you tell me how do you solved it?
Thank you very very much!! Kind regards,
Raquel
Dear SCRAN developers,
Hello, I am writing an issue because I have a questions.
genes <- !grepl(pattern = "^Rp[l|s]|Mt", x = rownames(brca.sce))
I converted the single cell seurat object as a reference into a SingleCellExperiment object (-> brca.sce) and used that data to save the "genes".mgs <- scoreMarkers(brca.sce, subset.row = genes)
After going through the scoremarkers function, this error occurred.I would really appreciate it if you let me know if there is a solution. Thank you!
Best, EUNHA