Idents(scRNA) <- scRNA$Majory_type subset(scRNA, cells = c("cell.1","cell.2","cell.3",...), invert = F) #根据cell.id提取 subset(x = scRNA, idents = c("CD4 T cells", "CD8 T cells")) subset(x = scRNA, subset = nFeatures > 500 & PC1 > 5, idents = "B cells") subset(x = scRNA, subset = orig.ident == "Replicate1") subset(x = scRNA, downsample = 100) subset(x = scRNA, features = VariableFeatures(object = scRNA)) scRNA= scRNA[,scRNA@meta.data$seurat_clusters %in% c(0,2)] scRNA= scRNA[, Idents(scRNA) %in% c( "T cell" , "B cell" )]

矩阵数据提取

#assay数据提取 GetAssayData( scRNA, slot = "counts") scRNA<- SetAssayData(scRNA, slot = "scale.data", new.data = new.data) #embeddings 数据提取 Embeddings(object = scRNA, reduction = "pca") # FetchData can pull anything from expression matrices, cell embeddings, or metadata FetchData(object = scRNA, vars = c("PC_1", "percent.mito")) exprs <- data.frame(FetchData(object = scRNA, vars = VariableFeatures(object = scRNA))) exprs <- t(exprs) #行列变换 write.csv(exprs,file = 'exprs.csv')