CellCycleScoring: Score cell cycle phases
In Seurat: Tools for Single Cell Genomics

CellCycleScoring

R Documentation

Score cell cycle phases

Description

Score cell cycle phases

Usage

CellCycleScoring(
  object,
  s.features,
  g2m.features,
  ctrl = NULL,
  set.ident = FALSE,
  ...
)

Arguments

`object`	A Seurat object
`s.features`	A vector of features associated with S phase
`g2m.features`	A vector of features associated with G2M phase
`ctrl`	Number of control features selected from the same bin per analyzed feature supplied to `AddModuleScore`. Defaults to value equivalent to minimum number of features present in 's.features' and 'g2m.features'.
`set.ident`	If true, sets identity to phase assignments Stashes old identities in 'old.ident'
`...`	Arguments to be passed to `AddModuleScore`

Value

A Seurat object with the following columns added to object meta data: S.Score, G2M.Score, and Phase

Examples

## Not run: 
data("pbmc_small")
# pbmc_small doesn't have any cell-cycle genes
# To run CellCycleScoring, please use a dataset with cell-cycle genes
# An example is available at http://satijalab.org/seurat/cell_cycle_vignette.html
pbmc_small <- CellCycleScoring(
  object = pbmc_small,
  g2m.features = cc.genes$g2m.genes,
  s.features = cc.genes$s.genes
)
head(x = pbmc_small@meta.data)

## End(Not run)

Seurat documentation built on May 29, 2024, 4:20 a.m.