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

In monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

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)

monocle documentation built on Nov. 8, 2020, 5:06 p.m.