将seurat对象转换为h5ad文件

在R中进行

library(Seurat)
library(SeuratDisk)

setwd('./all_dataTOh5ad/')
rna <- readRDS('./PBMC_scRNAseq.rds')
rna<-UpdateSeuratObject(rna)
table([email protected]$Severity,[email protected]$sample_assign)
rna_s<- rna[,[email protected]$Severity == 'severe']

## 因为我需要的是原始的counts数据
rna_s@assays$RNA@data <- rna_s@assays$RNA@counts

SaveH5Seurat(rna_s, filename = "severe_all.h5seurat")
Convert("severe_all.h5seurat", dest = "h5ad")

### 注意这里的提示
# Adding scale.data from RNA as X
# Transfering meta.features to var
# Adding data from RNA as raw
# Transfering meta.features to raw/var

## 将counts赋予data，在读入h5ad时，需要将raw.X赋值给.X,即obj=obj.raw.to_adata()，才代表counts数据，否则就是scale.data