exportSCE: Export data in SingleCellExperiment object

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Export data in SingleCellExperiment object

Description

Export data in SingleCellExperiment object

Usage

exportSCE(
  inSCE,
  samplename = "sample",
  directory = "./",
  type = "Cells",
  format = c("SCE", "AnnData", "FlatFile", "HTAN", "Seurat")
)

Arguments

inSCE	A SingleCellExperiment object that contains the data. QC metrics are stored in colData of the singleCellExperiment object.
samplename	Sample name. This will be used as name of subdirectories and the prefix of flat file output. Default is 'sample'.
directory	Output directory. Default is './'.
type	Type of data. The type of data stored in SingleCellExperiment object. It can be 'Droplets'(raw droplets matrix) or 'Cells' (cells matrix).
format	The format of output. It currently supports flat files, rds files and python h5 files. It can output multiple formats. Default: c("SCE", "AnnData", "FlatFile", "HTAN").

Value

Generates a file containing data from inSCE, in specified format.

Examples

data(scExample)
## Not run: 
exportSCE(sce, format = "SCE")

## End(Not run)

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.