exportSCEToSeurat: Export data in Seurat object

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

Export data in Seurat object

Description

Export data in Seurat object

Usage

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.

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