Error in FUN(x, table, nomatch = nomatch, incomparables = incomparables) : 'match' requires vector arguments

[galaxyeee]

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.

Error in FUN(x, table, nomatch = nomatch, incomparables = incomparables) : 
  'match' requires vector arguments

5. FUN(x, table, nomatch = nomatch, incomparables = incomparables)
4. match(desired.comparisons, averaged.comparisons)
3. match(desired.comparisons, averaged.comparisons)
2. .cross_reference_to_desired(pre.ave$averaged.comparisons, desired.comparisons, collapse.symmetric = collapse.symmetric)
1. scoreMarkers(brca.sce, row.data = genes, groups = brca.sce$celltype_major)

I would really appreciate it if you let me know if there is a solution. Thank you!

Best,
EUNHA

[LTLA]

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:

• Save 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.
• Separately, just try 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.

[galaxyeee]

Hi, @LTLA
Thanks to you, I solved problem!
Thank you.

Best,
EUNHA

[RaquelGRubio]

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