convertSCEToSeurat Converts sce object to seurat while retaining all assays and metadata

convertSCEToSeurat Converts sce object to seurat while retaining all assays and metadata

convertSCEToSeurat(
  inSCE,
  countsAssay = NULL,
  normAssay = NULL,
  scaledAssay = NULL,
  copyColData = FALSE,
  copyReducedDim = FALSE,
  copyDecontX = FALSE,
  pcaReducedDim = NULL,
  icaReducedDim = NULL,
  tsneReducedDim = NULL,
  umapReducedDim = NULL
)

Arguments

inSCE

A SingleCellExperiment object to convert to a Seurat object.

countsAssay

Which assay to use from sce object for raw counts. Default NULL.

normAssay

Which assay to use from sce object for normalized data. Default NULL.

scaledAssay

Which assay to use from sce object for scaled data. Default NULL.

copyColData

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

copyReducedDim

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

copyDecontX

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

pcaReducedDim

Specify a character value indicating the name of the reducedDim to store as default pca computation in the output seurat object. Default is NULL which will not store any reducedDim as the default pca. This will only work when copyReducedDim parameter is set to TRUE.

icaReducedDim

Specify a character value indicating the name of the reducedDim to store as default ica computation in the output seurat object. Default is NULL which will not store any reducedDim as the default ica. This will only work when copyReducedDim parameter is set to TRUE.

tsneReducedDim

Specify a character value indicating the name of the reducedDim to store as default tsne computation in the output seurat object. Default is NULL which will not store any reducedDim as the default tsne. This will only work when copyReducedDim parameter is set to TRUE.

umapReducedDim

Specify a character value indicating the name of the reducedDim to store as default umap computation in the output seurat object. Default is NULL which will not store any reducedDim as the default umap. This will only work when copyReducedDim parameter is set to TRUE.

Value

Updated seurat object that contains all data from the input sce object

Examples

data(scExample, package = "singleCellTK")
seurat <- convertSCEToSeurat(sce)
#> The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
#> which was just loaded, will retire in October 2023.
#> Please refer to R-spatial evolution reports for details, especially
#> https://r-spatial.org/r/2023/05/15/evolution4.html.
#> It may be desirable to make the sf package available;
#> package maintainers should consider adding sf to Suggests:.
#> The sp package is now running under evolution status 2
#>      (status 2 uses the sf package in place of rgdal)