convertSCEToSeurat {singleCellTK} | R Documentation

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

### Description

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

### Usage

    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)

[Package singleCellTK version 2.2.0 Index]