b.limour.top/source/_posts/导出singler需要的数据.md

---

title: 导出SingleR需要的数据 tags: [] id: '2045' categories:

• • uncategorized

    date: 2022-10-03 17:06:30

    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')