Open Zepeng-Mu opened 5 years ago
Hi,
If you use the CreateSinglerSeuratObject function it creates a Seurat object before creating a SingleR object. If you already have a Seurat Object use the CreateSinglerObject function. Both are explained here.
Best, Dvir
This is really helpful. Thanks!
Hi, I am now creating a singleR object from my Seurat object.
singler <- CreateSinglerObject(
counts = as.matrix(GetAssayData(seuratDt, slot = "counts", assay = "RNA")),
annot = seuratDt@meta.data$seurat_clusters,
project.name = "ST83_integrated",
min.genes = 0,
technology = "10X",
species = "Human",
ref.list = NULL,
normalize.gene.length = F
)
singler$seurat <- seuratDt
singler$meta.data$orig.ident = seuratDt@meta.data$orig.ident
singler$meta.data$xy = seuratDt@reductions$umap@cell.embeddings
singler$meta.data$clusters = seuratDt@active.ident
But convertSingleR2Browser
reports an error: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
.
How could I solve this?
Thank you so much!
Not sure what is going on. Try annot = NULL
instead.
Unfortunately, annot = NULL
does not work either.
Hi,
I am wondering whether singleR re-do PCA and clustering on my original Seurat object. Based on UMAP, the output from singleR is different from my Seurat object. But I do not think this is mentioned in the singleR method. Maybe I messed up my dataset, so I just want to make sure.
Thank you so much!