Export data in SingleCellExperiment object

Export data in SingleCellExperiment object

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)
if (FALSE) {
exportSCE(sce, format = "SCE")
}