seurat_to_cds: seurat_to_cds

In alxsully/Sentinel: Test package for Seurat helper functions

Description

Converts Seurat object to preprocessed cds.

Usage

seurat_to_cds(
  seurat,
  assay = "SCT",
  preprocess = TRUE,
  dims = 50,
  norm = "none",
  import_umap = TRUE
)

Arguments

seurat	The Seurat object to be converted.
assay	Assay within the Seurat object to be imported.
preprocess	Determines whether the new cds will be preprocessed. Default is TRUE.
dims	Number of principal components returned after preprocessing.
norm	Normalization method used in preprocess_cds. Default is "none".
import_umap	Imports UMAP projection into the cell data set object. Default is TRUE.

Details

Seurat to cell data set conversion function. This function takes in a Seurat object and returns a cell data set object. Automatically runs PCA on the new cell data set object.

I've only included this to stop warnings from document()

Value

A cell data set (cds) object

Examples

new_cds <- seurat_to_cds(Seurat.object, assay = "SCT")

alxsully/Sentinel documentation built on May 30, 2021, 4:15 a.m.