Seurat: as.Seurat – R documentation

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Seurat

as.Seurat

Convert objects to Seurat objects

Description

Convert objects to Seurat objects

Usage

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

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

Arguments

`x`	An object to convert to class `Seurat`
`slot`	Slot to store expression data as
`assay`	Name to store expression matrices as
`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

Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]

Initial release

2021-03-17