Open sidrahmaryam-cyber opened 1 year ago
seuratObj@assays$RNA@counts
is a structure of Seurat Object. Maybe your use some methods such like harmony etc., store the data in another slot, but not RNA. Actually, the function CreateObject_fromSeurat()
is designed just to get expression data and cell label.
You can use code followed exchange one code data <- as.matrix(Seurat::GetAssayData(object = Seurat.object, slot = slot, assay = "RNA"))
:
data <- as.matrix(Seurat::GetAssayData(object = Seurat.object, slot = slot, assay = 'RNA'))
myCelltype <- as.character(Seurat.object@meta.data[,cell_type])
data <- as.data.frame(data)
colnames(data) <- paste(1:length(myCelltype), myCelltype, sep = "_")
mt <- CreateNichConObject(data=data, min.feature = 0,
names.field = 2,
names.delim = "_",
source = your_source, # "fullLength", "UMI", "TPM"
scale.factor = scale.factor,
Org = Org,
project = "Microenvironment")
I am just a beginner in scientific research, and I recognize that the R package I developed has various shortcomings. I am very grateful for any feedback and suggestions for improvement that everyone provides.
Best wishes!
Hello, I have been using this tool for some time now. And it has really given good results. However, right now I was running the same script I always have had to a new data, and while using CreateObject_fromSeurat,
I get this error : Error: 'RNA' is not an assay
I know the assay name is not RNA here, but originalexp, however I have been using it previously with such name, and it worked smooth. Can you please suggest why it gave this issue now.
Thank you!