R/seuratFunctions.R
convertSCEToSeurat.Rd
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
)
A SingleCellExperiment
object to convert to a Seurat
object.
Which assay to use from sce object for raw counts.
Default NULL
.
Which assay to use from sce object for normalized data.
Default NULL
.
Which assay to use from sce object for scaled data.
Default NULL
.
Boolean. Whether copy 'colData' of SCE object to
the 'meta.data' of Seurat object. Default FALSE
.
Boolean. Whether copy 'reducedDims' of the SCE
object to the 'reductions' of Seurat object. Default FALSE
.
Boolean. Whether copy 'decontXcounts' assay of the
SCE object to the 'assays' of Seurat object. Default TRUE
.
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
.
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
.
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
.
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
.
Updated seurat object that contains all data from the input sce object
data(scExample, package = "singleCellTK")
seurat <- convertSCEToSeurat(sce)