Seurat的各种数据成员访问
转自:https://www.jianshu.com/p/44c1f526e450
1.处理流程
data.count = Read10X(data.dir = "...") data = CreateSeuratObject(counts = data.count, min.cells = 3, min.features = 200) data = NormalizeData(object = data) data = FindVariableFeatures(object = data) data = ScaleData(object = data) data = RunPCA(object = data) data = FindNeighbors(object = data) data = FindClusters(object = data, resolution = 0.8)
2.访问
raw counts,是cellranger或者其他计数软件得到的原始count文件:
data@assays$RNA@counts
经过文库标准化并且经过log transformed data的数据:
data@assays$RNA@data
data@assays$RNA@scale.data
3.降维聚类
细胞类型:
data@active.ident
这里表示的是降维聚类后,每一类所拥有的细胞,或者说是每一类各对应哪些细胞。
#pca降维 data@reductions$pca@cell.embeddings #umap降维 data@reductions$umap@cell.embeddings