R: Create a 'Seurat' object

CreateSeuratObject {SeuratObject} | R Documentation

## Create a `Seurat` object

### 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,
      row.names = NULL,
      ...
    )

    ## 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. Row names in the metadata need to match the column names of the counts matrix.
`...` | 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.
`row.names` | When `counts` is a `data.frame` or `data.frame`-derived object: an optional vector of feature names to be used

### 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

    ## Not run:
    pbmc_raw <- read.table(
      file = system.file('extdata', 'pbmc_raw.txt', package = 'Seurat'),
      as.is = TRUE
    )
    pbmc_small <- CreateSeuratObject(counts = pbmc_raw)
    pbmc_small

    ## End(Not run)

[Package SeuratObject version 4.0.3 Index]