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| 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')
|