Create a Seurat object
Create a Seurat object from raw data
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, ... )
counts |
Either a |
project |
Project name for the |
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.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 |
... |
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 |
A Seurat object
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.
## 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.