CreateSeuratObject | R Documentation |
Seurat
objectCreate a Seurat
object from raw data
CreateSeuratObject(
counts,
assay = "RNA",
names.field = 1,
names.delim = "_",
meta.data = NULL,
project = "CreateSeuratObject",
...
)
## Default S3 method:
CreateSeuratObject(
counts,
assay = "RNA",
names.field = 1L,
names.delim = "_",
meta.data = NULL,
project = "SeuratProject",
min.cells = 0,
min.features = 0,
...
)
## S3 method for class 'Assay'
CreateSeuratObject(
counts,
assay = "RNA",
names.field = 1L,
names.delim = "_",
meta.data = NULL,
project = "SeuratProject",
...
)
## S3 method for class 'Assay5'
CreateSeuratObject(
counts,
assay = "RNA",
names.field = 1L,
names.delim = "_",
meta.data = NULL,
project = "SeuratProject",
...
)
counts |
Either a |
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 |
project |
Project name for the |
... |
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 |
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)
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