R package：SingleR自动注释单细胞类群

BiocManager::install("SingleR")
BiocManager::install("celldex")
library(SingleR)
library(celldex)
?SingleR
?MouseRNAseqData()
ref.se=MouseRNAseqData()
ref.se
pred = SingleR(test = pbmc@assays$RNA@data, ref = ref.se,
               labels = ref.se$label.fine, method = "cluster", 
               clusters = pbmc@active.ident, 
               assay.type.test = "logcounts", assay.type.ref = "logcounts")
table(pred$labels)
celltype = data.frame(ClusterID=rownames(pred), 
                      celltype=pred$labels, stringsAsFactors = F) 
pbmc@meta.data$singleR=celltype[match(pbmc@active.ident,celltype$ClusterID),'celltype']
DimPlot(pbmc, reduction = "tsne", group.by = "singleR")