exportCDS: Export a monocle CellDataSet object to other popular single...

Description Usage Arguments Value Examples

View source: R/cds_conversion.R

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

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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

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## 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)

cole-trapnell-lab/monocle-release documentation built on May 13, 2019, 8:50 p.m.