monocle3_to_seurat: Monocle3 to Seurat

In scfurl/viewmaster: This package aims annotate scRNAseq data according to a reference

Monocle3 to Seurat

Description

Conver Monocle3 cell data set to a Seurat object. For a variety of reasons, the recommendations are to use this funciont only to generate skeleton Seurat objects that can be used for plotting and not much else. The resulting object will not contain PCA reducitons or nearest neighbor graphs.

Usage

monocle3_to_seurat(
  cds,
  seu_rd = "umap",
  mon_rd = "UMAP",
  assay_name = "RNA",
  row.names = "gene_short_name",
  normalize = T
)

Arguments

seu_rd	Reduced dimname for seurat ('i.e. UMAP')
mon_rd	Reduced dimname for monocle3 ('i.e. UMAP')
assay_name	Name of data slot ('i.e. RNA')
row.names	rowData column to use as rownames for Seurat object
seu	Seurat Object

Value

a cell_data_set object

scfurl/viewmaster documentation built on Nov. 22, 2022, 2:59 p.m.