convertSCEToSeurat {singleCellTK} | R Documentation |
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 )
inSCE |
A |
countsAssay |
Which assay to use from sce object for raw counts.
Default |
normAssay |
Which assay to use from sce object for normalized data.
Default |
scaledAssay |
Which assay to use from sce object for scaled data.
Default |
copyColData |
Boolean. Whether copy 'colData' of SCE object to
the 'meta.data' of Seurat object. Default |
copyReducedDim |
Boolean. Whether copy 'reducedDims' of the SCE
object to the 'reductions' of Seurat object. Default |
copyDecontX |
Boolean. Whether copy 'decontXcounts' assay of the
SCE object to the 'assays' of Seurat object. Default |
pcaReducedDim |
Specify a character value indicating the name of
the reducedDim to store as default pca computation in the output seurat
object. Default is |
icaReducedDim |
Specify a character value indicating the name of
the reducedDim to store as default ica computation in the output seurat
object. Default is |
tsneReducedDim |
Specify a character value indicating the name of
the reducedDim to store as default tsne computation in the output seurat
object. Default is |
umapReducedDim |
Specify a character value indicating the name of
the reducedDim to store as default umap computation in the output seurat
object. Default is |
Updated seurat object that contains all data from the input sce object
data(scExample, package = "singleCellTK") seurat <- convertSCEToSeurat(sce)