##scRNA_harmony0620注释后-FINAL.Rdata ##从这个文件开始使用 ##scRNAseq分析文件2 ##inferCNV需要四个对象 ##1.单细胞原始 counts 矩阵 ##2.细胞注释文件 ##3.hg38基因位置文件 ##系统报错改为英文 Sys.setenv(LANGUAGE = "en") ##禁止转化为因子 options(stringsAsFactors = FALSE) ##清空环境 rm(list=ls()) library(Seurat) library(tidyverse) library(dplyr) library(ggplot2) library(patchwork) library(cowplot) library(SingleR) library(celldex) library(clustree) library(scDblFinder) load("~/scRNAseq/scRNA_harmony0620注释后-FINAL.Rdata") scRNA1 <- scRNA_harmony ##1.单细胞原始 counts 矩阵 counts_matrix <- LayerData( scRNA1, assay = "RNA", layer = "counts" ) class(counts_matrix) ##2.细胞注释文件 table(scRNA_harmony$celltype.1) cell_annotations <- data.frame( celltype = scRNA1$celltype.1, row.names = colnames(scRNA1), stringsAsFactors = FAL