Creates Seurat object from 10X cell ranger output

Creates Seurat object from 10X cell ranger output

createSeuratObjectPipeline(
  data.dir = "~/filtered_feature_bc_matrix",
  nFeature_RNA_lower = 500,
  nFeature_RNA_upper = 5000,
  percent.mt = 5,
  nfeatures = 2000,
  dims = 20,
  clusterResolution = 0.8
)

Arguments

data.dir

Directory where data is stored. Default "~/filtered_feature_bc_matrix".
nFeature_RNA_lower

Lower bound of nFeature_RNA. Default 500.
nFeature_RNA_upper

Upper bound of nFeature_RNA. Default 5000.
percent.mt

Upper bound of percentage of mitochondria genes. Default 5.
nfeatures

Number of top most variable genes. Default 2000.
dims

Number of dimensions for finding neighbors and UMAP. Default 20.
clusterResolution

Cluster resolution for finding clusters. Default 0.8.

Value

Seurat Object with pca and UMAP calculated, ready for use with predictCells().

Author

Kimberle Shen