CreateSeuratObject: Create a Seurat object
In atakanekiz/Seurat3.0: Tools for Single Cell Genomics

Description Usage Arguments Details Examples

Create a Seurat object from a feature (e.g. gene) expression matrix. The expected format of the input matrix is features x cells.

1
2
3

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

`counts`	Unnormalized data such as raw counts or TPMs
`project`	Sets the project name for the Seurat object.
`assay`	Name of the assay corresponding to the initial input data.
`min.cells`	Include features detected in at least this many cells. Will subset the counts matrix as well. To reintroduce excluded features, create a new object with a lower cutoff.
`min.features`	Include cells where at least this many features are detected.
`names.field`	For the initial identity class for each cell, choose this field from the cell's name. E.g. If your cells are named as BARCODE_CLUSTER_CELLTYPE in the input matrix, set names.field to 3 to set the initial identities to CELLTYPE.
`names.delim`	For the initial identity class for each cell, choose this delimiter from the cell's column name. E.g. If your cells are named as BARCODE-CLUSTER-CELLTYPE, set this to "-" to separate the cell name into its component parts for picking the relevant field.
`meta.data`	Additional cell-level metadata to add to the Seurat object. Should be a data frame where the rows are cell names and the columns are additional metadata fields.

Note: In previous versions (<3.0), this function also accepted a parameter to set the expression threshold for a 'detected' feature (gene). This functionality has been removed to simplify the initialization process/assumptions. If you would still like to impose this threshold for your particular dataset, simply filter the input expression matrix before calling this function.

pbmc_raw <- read.table(
  file = system.file('extdata', 'pbmc_raw.txt', package = 'Seurat3.0'),
  as.is = TRUE
)
pbmc_small <- CreateSeuratObject(counts = pbmc_raw)
pbmc_small