16 Automated annotation with SingleR
Automated cell type labels are assigned using SingleR with the Human Primary Cell Atlas as the reference dataset. SingleR uses a correlation-based approach to compare each cell’s expression profile against bulk reference profiles and assigns the label of the most similar reference cell type. The labels are added to the Seurat object metadata and visualised on the WNN UMAP.
library(SingleCellExperiment)
library(SingleR)
library(celldex)
sce <- as.SingleCellExperiment(combined)
ref.set <- celldex::HumanPrimaryCellAtlasData()
pred.cnts <- SingleR::SingleR(test = sce,
ref = ref.set,
labels = ref.set$label.main)
combined@meta.data$SingleR.labels <- pred.cnts$labels
