Seurat2SCseq: Converting a Seurat object to a RaceID/VarID object

In RaceID: Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Converting a Seurat object to a RaceID/VarID object

Description

This function expects a class Seurat object from the Seurat package as input and converts this into a RaceID SCseq object. The function transfers the counts, initializes ndata and fdata without further filtering, transfers the PCA cell embeddings from the Seurat object to dimRed, transfers the clustering partition, and umap and tsne dimensional reduction (if available). CAUTION: Cluster numbers in RaceID start at 1 by default. Hence, all Seurat cluster numbers are shifted by 1.

Usage

Seurat2SCseq(Se, rseed = 12345)

Arguments

Se	Seurat object.
rseed	Integer number. Random seed for sampling cluster colours.

Value

RaceID SCseq object.

RaceID documentation built on Sept. 28, 2023, 5:06 p.m.