小鼠自动注释

###########################SingleR对小鼠免疫单细胞自动注释

#install.packages("remotes")

#library(remotes)

#remotes::install_github("LTLA/celldex")

BiocManager::install("celldex")

library(SingleR)

library(celldex)

sce_for_SingleR <- GetAssayData(Myeloid, slot="data")

clusters=Myeloid@meta.data$seurat_clusters

#############第一个数据集

mouseImmu <- ImmGenData()#获取数据集，2021-05-18

pred.mouseImmu <- SingleR(test = sce_for_SingleR, ref = mouseImmu, labels = mouseImmu$label.main,

                          method = "cluster", clusters = clusters,

                          assay.type.test = "logcounts", assay.type.ref = "logcounts")

#################第二个数据集

mouseRNA <- MouseRNAseqData()#获取数据集，2021-05-18

pred.mouseRNA <- SingleR(test = sce_for_SingleR, ref = mouseRNA, labels = mouseRNA$label.fine ,

                        method = "cluster", clusters = clusters,

                        assay.type.test = "logcounts", assay.type.ref = "logcounts")

cellType=data.frame(ClusterID=levels(Myeloid@meta.data$seurat_clusters),

                    mouseImmu=pred.mouseImmu$labels,

                    mouseRNA=pred.mouseRNA$labels )