R中seurat等问题学习

1.Seurat

转自：https://cloud.tencent.com/developer/article/1055892

# Initialize the Seurat object with the raw (non-normalized data).  Keep all
# genes expressed in >= 3 cells (~0.1% of the data). Keep all cells with at
# least 200 detected genes
pbmc <- CreateSeuratObject(raw.data = pbmc.data, min.cells = 3, min.genes = 200, 
    project = "10X_PBMC")

这里的min.genes是对细胞来说的，只包含至少能检测到3个基因的细胞。

min.cells=200，只包含至少在200个cell中检测到的基因。

Seurat包的默认参数：

CreateSeuratObject(
  counts,
  project = "SeuratProject",
  assay = "RNA",
  min.cells = 0,
  min.features = 0,
  names.field = 1,
  names.delim = "_",
  meta.data = NULL
)

https://www.rdocumentation.org/packages/Seurat/versions/3.1.4/topics/CreateSeuratObject