Export data in Seurat object

Export data in Seurat object

exportSCEToSeurat(
  inSCE,
  prefix = "sample",
  outputDir = "./",
  overwrite = TRUE,
  copyColData = TRUE,
  copyReducedDim = TRUE,
  copyDecontX = TRUE
)

Arguments

inSCE

A SingleCellExperiment object that contains the data. QC metrics are stored in colData of the singleCellExperiment object.

prefix

Prefix to use for the name of the output file. Default "sample".

outputDir

Path to the directory where outputs will be written. Default is the current working directory.

overwrite

Boolean. Whether overwrite the output if it already exists in the outputDir. Default TRUE.

copyColData

Boolean. Whether copy 'colData' of SCE object to the 'meta.data' of Seurat object. Default TRUE.

copyReducedDim

Boolean. Whether copy 'reducedDims' of the SCE object to the 'reductions' of Seurat object. Default TRUE.

copyDecontX

Boolean. Whether copy 'decontXcounts' assay of the SCE object to the 'assays' of Seurat object. Default TRUE.

Value

Generates a Seurat object containing data from inSCE.