Create a Seurat object — CreateSeuratObject • SeuratObject

Create a Seurat object from raw data

CreateSeuratObject(
  counts,
  assay = "RNA",
  names.field = 1,
  names.delim = "_",
  meta.data = NULL,
  project = "CreateSeuratObject",
  ...
)

# S3 method for default
CreateSeuratObject(
  counts,
  assay = "RNA",
  names.field = 1L,
  names.delim = "_",
  meta.data = NULL,
  project = "SeuratProject",
  min.cells = 0,
  min.features = 0,
  ...
)

# S3 method for Assay
CreateSeuratObject(
  counts,
  assay = "RNA",
  names.field = 1L,
  names.delim = "_",
  meta.data = NULL,
  project = "SeuratProject",
  ...
)

# S3 method for Assay5
CreateSeuratObject(
  counts,
  assay = "RNA",
  names.field = 1L,
  names.delim = "_",
  meta.data = NULL,
  project = "SeuratProject",
  ...
)

Arguments

counts: Either a matrix-like object with unnormalized data with cells as columns and features as rows or an Assay-derived object
assay: Name of the initial assay
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. Row names in the metadata need to match the column names of the counts matrix.
project: Project name for the Seurat object
...: Arguments passed to other methods
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

Value

A Seurat object

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.

Examples

if (FALSE) {
pbmc_raw <- read.table(
  file = system.file('extdata', 'pbmc_raw.txt', package = 'Seurat'),
  as.is = TRUE
)
pbmc_small <- CreateSeuratObject(counts = pbmc_raw)
pbmc_small
}