exportCDS {monocle} | R Documentation

## Export a monocle CellDataSet object to other popular single cell analysis toolkit.

### Description

This function takes a monocle CellDataSet and converts it to another type of object used in another popular single cell analysis toolkit. It currently supports Scran and Seurat packages.

### Usage

    exportCDS(monocle_cds, export_to = c("Seurat", "Scater"),
      export_all = FALSE)

### Arguments

`monocle_cds` | the Monocle CellDataSet you would like to export into a type used in another package
`export_to` | the object type you would like to export to, either Seurat or Scater
`export_all` | Whether or not to export all the slots in Monocle and keep in another object type. Default is FALSE (or only keep minimal dataset). If export_all is setted to be true, the original monocle cds will be keeped in the other cds object too. This argument is also only applicable when export_to is Seurat.

### Value

a new object in the format of another package, as described in the export_to argument.

### Examples

    ## Not run:
    lung <- load_lung()
    seurat_lung <- exportCDS(lung)
    seurat_lung_all <- exportCDS(lung, export_all = T)
    scater_lung <- exportCDS(lung, export_to = 'Scater')
    scater_lung_all <- exportCDS(lung, export_to = 'Scater', export_all = T)

    ## End(Not run)

[Package monocle version 2.12.0 Index]