CreateSeuratObject: Create a 'Seurat' object

In Seurat: Tools for Single Cell Genomics

Description

Create a Seurat object from raw data

Usage

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

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

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

Arguments

counts	Either a matrix-like object with unnormalized data with cells as columns and features as rows or an Assay-derived object
project	Project name for the Seurat 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.
...	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

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

Seurat documentation built on Jan. 13, 2021, 7:11 p.m.