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 )
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
#> Warning: replacing previous import 'spatstat.utils::RelevantNA' by 'spatstat.sparse::RelevantNA' when loading 'spatstat.core'#> Warning: replacing previous import 'spatstat.utils::grokIndexVector' by 'spatstat.sparse::grokIndexVector' when loading 'spatstat.core'#> Warning: replacing previous import 'spatstat.utils::fullIndexSequence' by 'spatstat.sparse::fullIndexSequence' when loading 'spatstat.core'#> Warning: replacing previous import 'spatstat.utils::positiveIndex' by 'spatstat.sparse::positiveIndex' when loading 'spatstat.core'#> Warning: replacing previous import 'spatstat.utils::replacementIndex' by 'spatstat.sparse::replacementIndex' when loading 'spatstat.core'#> Warning: replacing previous import 'spatstat.utils::RelevantEmpty' by 'spatstat.sparse::RelevantEmpty' when loading 'spatstat.core'#> Warning: replacing previous import 'spatstat.utils::isRelevantZero' by 'spatstat.sparse::isRelevantZero' when loading 'spatstat.core'#> Warning: replacing previous import 'spatstat.utils::logicalIndex' by 'spatstat.sparse::logicalIndex' when loading 'spatstat.core'#> Warning: replacing previous import 'spatstat.utils::RelevantZero' by 'spatstat.sparse::RelevantZero' when loading 'spatstat.core'#> Warning: replacing previous import 'spatstat.utils::strictIndexSequence' by 'spatstat.sparse::strictIndexSequence' when loading 'spatstat.core'#>#> #>