exportCDS {monocle} | R Documentation |
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.
exportCDS(monocle_cds, export_to = c("Seurat", "Scater"), export_all = FALSE)
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. |
a new object in the format of another package, as described in the export_to argument.
## 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)