Issue in findmarkergene function

[s-yadav21]

First of all, thank you for creating this package for single cell annotation.
I was trying to annotate my single cell dataset using you package and encountered following error:

clu_markers <- findmarkergenes(dif.PAC, species = "Human", cluster = 'All', match_CellMatch = TRUE, cancer = "Pancreatic Ductal Adenocarcinomas", tissue = "Pancreas", cell_min_pct = 0.25, logfc = 0.25, pvalue = 0.05)
`Note: the raw data matrix includes 14308 cells and 19823 genes.

---Revising gene symbols according to NCBI Gene symbols (updated in June 19, 2020, https://www.ncbi.nlm.nih.gov/gene) and no matched genes and duplicated genes will be removed.

Note: the new data matrix includes 14308 cells and 16587 genes.

Warning: there are only 1 potential marker genes in CellMatch database for Human Pancreatic Ductal Adenocarcinomas on Pancreas!
Error in if (nrow(ndata) == 0) { : argument is of length zero`

I am using a normalized Seurat object with cluster details. Could you please let me know what could be possible wrong?

[multitalk]

I‘m so sorry for my delay in writing back, but I've been very busy working recently. Actually this is because there are only 1 potential marker genes in CellMatch database. You can try v3.0 now since it allows you to use different combination of tissues to generate more potential marker genes.

[ranojoychatterjee]

Hi All,
I was trying to annotate my single cell data using scCATCH package but I encountered this following error:
code: clu_markers <- findmarkergenes(object = pbmc, species = 'Mouse', cluster = 'All', match_CellMatch = TRUE, cancer =
NULL, tissue = NULL, cell_min_pct = 0.25, logfc = 0.25, pvalue = 0.05)
error: Error in findmarkergenes(object = pbmc.data, species = "Mouse", cluster = "All", :
could not find function "findmarkergenes"
Note: I have already used the package to annotate this same data, but when I rerun the code I keep on facing this issue. Could you possibly tell me where I am going wrong?

[multitalk]

Hello, you can re-install scCATCH v3.0 and follow the user guide.

[ranojoychatterjee]

Firstly thank you for helping me. I re-installed the package, but it now shows an error:
Error in findmarkergene(object = pbmc, species = "Mouse", cluster = "All", :
unused argument (match_CellMatch = TRUE)

[multitalk]

Some parameters have been changed. No cluster exists. You can try the following code：

obj <- findmarkergene(object = pbmc, species = "Mouse", marker = cellmatch, tissue = "Blood")