no slot of name "counts" for this object of class "Assay5"

[andreyurch]

res<-scgsva(pbmc,df,method="ssgsea",useTerm=F)
Error in scgsva(pbmc, df, method = "ssgsea", useTerm = F) :
no slot of name "counts" for this object of class "Assay5"

But if I check:

pbmc
An object of class Seurat
26577 features across 2400 samples within 1 assay
Active assay: RNA (26577 features, 2000 variable features)
3 layers present: counts, data, scale.data
2 dimensional reductions calculated: pca, umap

[guokai8]

Hi @andreyurch ,
I updated the codes, and it should be fine now. Please install the newest version.
K

[zarnazhadi]

Hi,

I'm still having the same error "no slot of name "counts" for this object of class "Assay5"" when using the genes() function. My Seurat object consists of multiple objects joined together using JoinLayers(). When using a single object, genes() seems to work. Is there any way to execute findPathways on a joined/integrated Seurat object?

sample_norm <- readRDS("sample_norm.rds")
sample_norm <- JoinLayers(sample_norm)

res <- scgsva(sample_norm, hsko, method = "ssgsea")

heatmap <- scGSVA::Heatmap(res,group_by="condition", cluster_cols = F, show_colnames = F)

pathways <- findPathway(res, group = "condition")

sig_pathways <- sigPathway(res, group = "condition")

scGSVA::genes(res, features = "Natural.killer.cell.mediated.cytotoxicity", with.expr = F)

Thanks,
Zarnaz

[guokai8]

Hi @zarnazhadi,
Will check this these two days
K

[guokai8]

Hi @zarnazhadi ,
Please use the most update version(0.0.21) which fixed the issue.
K