Convert: Convert Seurat objects to other classes and vice versa

In atakanekiz/Seurat3.0: Tools for Single Cell Genomics

Description

Currently, we support direct conversion to/from loom (http://loompy.org/), SingleCellExperiment (https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html), and Anndata(https://anndata.readthedocs.io/en/latest/) objects.

Usage

as.Seurat(from, ...)

as.SingleCellExperiment(from, ...)

Convert(from, ...)

## S3 method for class 'SingleCellExperiment'
as.Seurat(from, counts = "counts",
  data = "logcounts", ...)

## S3 method for class 'Seurat'
as.SingleCellExperiment(from, assay = NULL, ...)

## S3 method for class 'anndata.base.AnnData'
Convert(from, to, X.slot = "scale.data",
  raw.slot = "data", ...)

## S3 method for class 'seurat'
Convert(from, to, filename, chunk.dims = "auto",
  chunk.size = 1000, overwrite = FALSE, display.progress = TRUE,
  anndata.raw = "raw.data", anndata.X = "data", ...)

Arguments

from	Object to convert from
...	Arguments passed to other methods
counts	name of the SingleCellExperiment assay to slot into @counts
data	name of the SingleCellExperiment assay to slot into @data
assay	Assay to convert
to	Class of object to convert to
X.slot	Seurat slot to transfer anndata X into. Default is scale.data
raw.slot	Seurat slot to transfer anndata raw into. Default is data
filename	Filename for writing files
chunk.dims	Internal HDF5 chunk size
chunk.size	Number of cells to stream to loom file at a time
overwrite	Overwrite existing file at filename?
display.progress	Display a progress bar
anndata.raw	Name of matrix (raw.data, data) to put in the anndata raw slot
anndata.X	Name of matrix (data, scale.data) to put in the anndata X slot

Value

An object of class to

atakanekiz/Seurat3.0 documentation built on May 26, 2019, 2:33 a.m.