Convert objects to Seurat objects

Source: R/objects.R

Convert objects to Seurat objects

# S3 method for CellDataSet
as.Seurat(x, slot = "counts", assay = "RNA", verbose = TRUE, ...)

# S3 method for SingleCellExperiment
as.Seurat(
  x,
  counts = "counts",
  data = "logcounts",
  assay = NULL,
  project = "SingleCellExperiment",
  ...
)

Arguments

x

An object to convert to class Seurat

slot

Slot to store expression data as

assay

Name of assays to convert; set to NULL for all assays to be converted

verbose

Show progress updates

...

Arguments passed to other methods

counts

name of the SingleCellExperiment assay to store as counts; set to NULL if only normalized data are present

data

name of the SingleCellExperiment assay to slot as data. Set to NULL if only counts are present

project

Project name for new Seurat object

Value

A Seurat object generated from x