导出singler需要的数据.md 570 B


title: 导出SingleR需要的数据 tags: [] id: '2394' categories:

    • 注释

      date: 2022-10-04 01:06:30

      tp_samples <- list.files('~/GEO/GSE193337')
      tp_dir <- file.path('~/GEO/GSE193337', tp_samples)
      names(tp_dir) <- tp_samples
      counts <- Seurat::Read10X(data.dir = tp_dir)
      sce <- Seurat::CreateSeuratObject(counts, project = 'prostate',
                          min.cells = 3, min.features = 200)
      rm(counts)
      gc()
      table(sce$orig.ident)
      sce <- Seurat::NormalizeData(sce)
      logumi <- Seurat::GetAssayData(sce, slot="data")
      saveRDS(logumi, 'logumi.rds')