PrepareForCellCycleRegression

This function calculates module scores for a curated set of cell cycle-related gene clusters from the ccAFv2 gene set. These scores can be used to regress out cell cycle effects from single-cell expression data.

PrepareForCellCycleRegression(
  seurat_obj,
  assay = "SCT",
  species = "human",
  gene_id = "ensembl"
)

Arguments	Range of Values	Description
seurat_obj	NA	a seurat object must be supplied to classify, no default
assay	‘SCT’,’RNA’, etc.	which seurat_obj assay to use for classification, helpful if data is pre-normalized, default is ‘SCT’
species	‘human’ or ‘mouse’	from which species did the samples originate, default is ‘human’
gene_id	‘ensembl’ or ‘symbol’	what type of gene ID is used, default is ‘ensembl’

Value

Returns the input Seurat object, with five new metadata columns containing module scores for the following cell cycle clusters (Late.G1, S, S.G2, G2.M, M.Early.G1)

These scores represent average expression of marker genes for each phase and can be used for downstream cell cycle regression.

Example

# Prepare Seurat object for cell cycle regression 
PrepareForCellCycleRegression(seurat_obj)

Example Use